data_16416 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex ; _BMRB_accession_number 16416 _BMRB_flat_file_name bmr16416.str _Entry_type original _Submission_date 2009-07-23 _Accession_date 2009-07-23 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Katoh Etsuko . . 2 Louis John M. . 3 Yamazaki Toshimasa . . 4 Gronenborn Angela M. . 5 Torchia Dennis A. . 6 Ishima Rieko . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count chemical_rates 1 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-06-06 original author . stop_ _Original_release_date 2012-06-06 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 12824484 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Katoh Etsuko . . 2 Louis John M. . 3 Yamazaki Toshimasa . . 4 Gronenborn Angela M. . 5 Torchia Dennis A. . 6 Ishima Rieko . . stop_ _Journal_abbreviation 'Protein Sci.' _Journal_name_full 'Protein science : a publication of the Protein Society' _Journal_volume 12 _Journal_issue 7 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1376 _Page_last 1385 _Year 2003 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'HIV-PR(D25N)-substrate C complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label HIV-PR(D25N) $HIV-PR 'substrate C' $substrate_C HIV-PR(D25N) $HIV-PR(D25N) stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_HIV-PR _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common HIV-PR _Molecular_mass . _Mol_thiol_state 'not reported' _Details 'HIV-1 protease construct with inactive site PR' ############################## # Polymer residue sequence # ############################## _Residue_count 99 _Mol_residue_sequence ; PQVTLWKRPLVTIKIGGQLK EALLDTGADDTVIEEMSLPG RWKPKMIGGIGGFIKVRQYD QIIIEIAGHKAIGTVLVGPT PVNVIGRNLLTQIGATLNF ; loop_ _Residue_seq_code _Residue_label 1 PRO 2 GLN 3 VAL 4 THR 5 LEU 6 TRP 7 LYS 8 ARG 9 PRO 10 LEU 11 VAL 12 THR 13 ILE 14 LYS 15 ILE 16 GLY 17 GLY 18 GLN 19 LEU 20 LYS 21 GLU 22 ALA 23 LEU 24 LEU 25 ASP 26 THR 27 GLY 28 ALA 29 ASP 30 ASP 31 THR 32 VAL 33 ILE 34 GLU 35 GLU 36 MET 37 SER 38 LEU 39 PRO 40 GLY 41 ARG 42 TRP 43 LYS 44 PRO 45 LYS 46 MET 47 ILE 48 GLY 49 GLY 50 ILE 51 GLY 52 GLY 53 PHE 54 ILE 55 LYS 56 VAL 57 ARG 58 GLN 59 TYR 60 ASP 61 GLN 62 ILE 63 ILE 64 ILE 65 GLU 66 ILE 67 ALA 68 GLY 69 HIS 70 LYS 71 ALA 72 ILE 73 GLY 74 THR 75 VAL 76 LEU 77 VAL 78 GLY 79 PRO 80 THR 81 PRO 82 VAL 83 ASN 84 VAL 85 ILE 86 GLY 87 ARG 88 ASN 89 LEU 90 LEU 91 THR 92 GLN 93 ILE 94 GLY 95 ALA 96 THR 97 LEU 98 ASN 99 PHE stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-09-30 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 1A94 "Structural Basis For Specificity Of Retroviral Proteases" 100.00 99 96.97 100.00 7.04e-61 PDB 1DAZ "Structural And Kinetic Analysis Of Drug Resistant Mutants Of Hiv-1 Protease" 100.00 99 96.97 98.99 3.17e-60 PDB 1DW6 "Structural And Kinetic Analysis Of Drug Resistant Mutants Of Hiv-1 Protease" 100.00 99 96.97 100.00 3.54e-61 PDB 1EBK "Structural And Kinetic Analysis Of Drug Resistant Mutants Of Hiv-1 Protease" 100.00 99 96.97 100.00 9.45e-61 PDB 1FEJ "Structural Implications Of Drug Resistant Mutants Of Hiv-1 Protease: High Resolution Crystal Structures Of The Mutant ProteaseS" 100.00 99 96.97 100.00 3.54e-61 PDB 1FF0 "Structural Implications Of Drug Resistant Mutants Of Hiv-1 Protease: High Resolution Crystal Structures Of The Mutant ProteaseS" 100.00 99 96.97 98.99 3.17e-60 PDB 1FFF "Structural Implications Of Drug Resistant Mutants Of Hiv-1 Protease : High Resolution Crystal Structures Of The Mutant Protease" 100.00 99 96.97 100.00 8.76e-61 PDB 1FFI "Structural Implications Of Drug Resistant Mutants Of Hiv-1 Protease: High Resolution Crystal Structures Of The Mutant ProteaseS" 100.00 99 96.97 100.00 8.76e-61 PDB 1FG6 "Structural Implications Of Drug Resistant Mutants Of Hiv-1 Protease: High Resolution Crystal Structures Of The Mutant ProteaseS" 100.00 99 96.97 100.00 1.02e-60 PDB 1FG8 "Structural Implications Of Drug Resistant Mutants Of Hiv-1 Protease: High Resolution Crystal Structures Of The Mutant ProteaseS" 100.00 99 96.97 100.00 1.02e-60 PDB 1FGC "Structural Implications Of Drug Resistant Mutants Of Hiv-1 Protease: High Resolution Crystal Structures Of The Mutant ProteaseS" 100.00 99 97.98 100.00 1.95e-61 PDB 1Q9P "Solution Structure Of The Mature Hiv-1 Protease Monomer" 95.96 95 97.89 100.00 5.49e-58 PDB 1SDT "Crystal Structures Of Hiv Protease V82a And L90m Mutants Reveal Changes In Indinavir Binding Site." 100.00 99 97.98 100.00 1.95e-61 PDB 1SDU "Crystal Structures Of Hiv Protease V82a And L90m Mutants Reveal Changes In Indinavir Binding Site." 100.00 99 96.97 100.00 3.54e-61 PDB 1SDV "Crystal Structures Of Hiv Protease V82a And L90m Mutants Reveal Changes In Indinavir Binding Site." 100.00 99 96.97 98.99 6.11e-61 PDB 2A1E "High Resolution Structure Of Hiv-1 Pr With Ts-126" 100.00 99 97.98 100.00 1.95e-61 PDB 2AOC "Crystal Structure Analysis Of Hiv-1 Protease Mutant I84v With A Substrate Analog P2-Nc" 100.00 99 98.99 100.00 1.14e-61 PDB 2AOD "Crystal Structure Analysis Of Hiv-1 Protease With A Substrate Analog P2-Nc" 100.00 99 97.98 100.00 1.95e-61 PDB 2AOE "Crystal Structure Analysis Of Hiv-1 Protease Mutant V82a With A Substrate Analog Ca-P2" 100.00 99 96.97 98.99 6.11e-61 PDB 2AOF "Crystal Structure Analysis Of Hiv-1 Protease Mutant V82a With A Substrate Analog P1-P6" 100.00 99 96.97 98.99 6.11e-61 PDB 2AOG "Crystal Structure Analysis Of Hiv-1 Protease Mutant V82a With A Substrate Analog P2-Nc" 100.00 99 96.97 98.99 6.11e-61 PDB 2AOH "Crystal Structure Analysis Of Hiv-1 Protease Mutant V82a With A Substrate Analog P6-Pr" 100.00 99 96.97 98.99 6.11e-61 PDB 2AOI "Crystal Structure Analysis Of Hiv-1 Protease With A Substrate Analog P1-P6" 100.00 99 97.98 100.00 1.95e-61 PDB 2AOJ "Crystal Structure Analysis Of Hiv-1 Protease With A Substrate Analog P6-Pr" 100.00 99 97.98 100.00 1.95e-61 PDB 2AVM "Kinetics, Stability, And Structural Changes In High Resolution Crystal Structures Of Hiv-1 Protease With Drug Resistant Mutatio" 100.00 99 96.97 100.00 5.13e-61 PDB 2AVO "Kinetics, Stability, And Structural Changes In High Resolution Crystal Structures Of Hiv-1 Protease With Drug Resistant Mutatio" 100.00 99 96.97 100.00 5.13e-61 PDB 2AVQ "Kinetics, Stability, And Structural Changes In High Resolution Crystal Structures Of Hiv-1 Protease With Drug Resistant Mutatio" 100.00 99 96.97 100.00 2.98e-61 PDB 2AVS "Kinetics, Stability, And Structural Changes In High Resolution Crystal Structures Of Hiv-1 Protease With Drug Resistant Mutatio" 100.00 99 96.97 100.00 2.98e-61 PDB 2AVV "Kinetics, Stability, And Structural Changes In High Resolution Crystal Structures Of Hiv-1 Protease With Drug Resistant Mutatio" 100.00 99 96.97 98.99 6.82e-61 PDB 2F80 "Hiv-1 Protease Mutant D30n Complexed With Inhibitor Tmc114" 100.00 99 96.97 100.00 8.76e-61 PDB 2F81 "Hiv-1 Protease Mutant L90m Complexed With Inhibitor Tmc114" 100.00 99 96.97 100.00 3.54e-61 PDB 2F8G "Hiv-1 Protease Mutant I50v Complexed With Inhibitor Tmc114" 100.00 99 96.97 100.00 2.98e-61 PDB 2G69 "Structure Of Unliganded Hiv-1 Protease F53l Mutant" 100.00 99 96.97 98.99 1.76e-60 PDB 2HB3 "Wild-Type Hiv-1 Protease In Complex With Potent Inhibitor Grl06579" 100.00 99 97.98 100.00 1.95e-61 PDB 2HS1 "Ultra-High Resolution X-Ray Crystal Structure Of Hiv-1 Protease V32i Mutant With Tmc114 (Darunavir) Inhibitor" 100.00 99 96.97 100.00 3.54e-61 PDB 2HS2 "Crystal Structure Of M46l Mutant Of Hiv-1 Protease Complexed With Tmc114 (Darunavir)" 100.00 99 96.97 100.00 7.44e-61 PDB 2IDW "Crystal Structure Analysis Of Hiv-1 Protease Mutant V82a With A Potent Non-Peptide Inhibitor (Uic-94017)" 100.00 99 96.97 98.99 6.11e-61 PDB 2IEN "Crystal Structure Analysis Of Hiv-1 Protease With A Potent Non-Peptide Inhibitor (Uic-94017)" 100.00 99 97.98 100.00 1.95e-61 PDB 2IEO "Crystal Structure Analysis Of Hiv-1 Protease Mutant I84v With A Potent Non-peptide Inhibitor (uic-94017)" 100.00 99 98.99 100.00 1.14e-61 PDB 2NMY "Crystal Structure Analysis Of Hiv-1 Protease Mutant V82a With A Inhibitor Saquinavir" 100.00 99 96.97 98.99 6.11e-61 PDB 2NMZ "Crystal Structure Analysis Of Hiv-1 Protease Mutant V82a With A Inhibitor Saquinavir" 100.00 99 96.97 98.99 6.11e-61 PDB 2NNK "Crystal Structure Analysis Of Hiv-1 Protease Mutant I84v With A Inhibitor Saquinavir" 100.00 99 98.99 100.00 1.14e-61 PDB 2NNP "Crystal Structure Analysis Of Hiv-1 Protease Mutant I84v With A Inhibitor Saquinavir" 100.00 99 98.99 100.00 1.14e-61 PDB 2QCI "Hiv-1 Protease Mutant D30n With Potent Antiviral Inhibitor Grl-98065" 100.00 99 96.97 100.00 8.76e-61 PDB 2QD6 "Hiv-1 Protease Mutant I50v With Potent Antiviral Inhibitor Grl-98065" 100.00 99 96.97 100.00 2.98e-61 PDB 2QD7 "Hiv-1 Protease Mutant V82a With Potent Antiviral Inhibitor Grl-98065" 100.00 99 96.97 98.99 6.11e-61 PDB 2QD8 "Hiv-1 Protease Mutant I84v With Potent Antiviral Inhibitor Grl-98065" 100.00 99 98.99 100.00 1.14e-61 PDB 2Z4O "Wild Type Hiv-1 Protease With Potent Antiviral Inhibitor Grl-98065" 100.00 99 97.98 100.00 1.95e-61 PDB 2ZYE "Structure Of Hiv-1 Protease In Complex With Potent Inhibitor Kni-272 Determined By Neutron Crystallography" 98.99 99 97.96 100.00 1.70e-60 PDB 3A2O "Crystal Structure Of Hiv-1 Protease Complexed With Kni-1689" 100.00 99 97.98 100.00 1.95e-61 PDB 3B7V "Hiv-1 Protease Complexed With Gem-Diol-Amine Tetrahedral Intermediate Nlltqi" 100.00 99 97.98 100.00 1.95e-61 PDB 3B80 "Hiv-1 Protease Mutant I54v Complexed With Gem-Diol-Amine Intermediate Nlltqi" 100.00 99 96.97 100.00 2.98e-61 PDB 3BVA "Cystal Structure Of Hiv-1 Active Site Mutant D25n And P2-Nc Analog Inhibitor" 100.00 99 96.97 100.00 8.76e-61 PDB 3BVB "Cystal Structure Of Hiv-1 Active Site Mutant D25n And Inhibitor Darunavir" 100.00 99 96.97 100.00 8.76e-61 PDB 3CYW "Effect Of Flap Mutations On Structure Of Hiv-1 Protease And Inhibition By Saquinavir And Darunavir" 100.00 99 96.97 98.99 2.69e-60 PDB 3CYX "Crystal Structure Of Hiv-1 Mutant I50v And Inhibitor Saquinavira" 100.00 99 96.97 100.00 2.98e-61 PDB 3D1X "Crystal Structure Of Hiv-1 Mutant I54m And Inhibitor Saquinavir" 100.00 99 96.97 100.00 4.22e-61 PDB 3D1Y "Crystal Structure Of Hiv-1 Mutant I54v And Inhibitor Saquina" 100.00 99 96.97 100.00 2.98e-61 PDB 3D1Z "Crystal Structure Of Hiv-1 Mutant I54m And Inhibitor Darunavir" 100.00 99 96.97 100.00 4.22e-61 PDB 3D20 "Crystal Structure Of Hiv-1 Mutant I54v And Inhibitor Darunavia" 100.00 99 96.97 100.00 2.98e-61 PDB 3DJK "Wild Type Hiv-1 Protease With Potent Antiviral Inhibitor Grl-0255a" 100.00 99 97.98 100.00 1.95e-61 PDB 3DK1 "Wild Type Hiv-1 Protease With Potent Antiviral Inhibitor Grl-0105a" 100.00 99 97.98 100.00 1.95e-61 PDB 3FX5 "Structure Of Hiv-1 Protease In Complex With Potent Inhibitor Kni-272 Determined By High Resolution X-ray Crystallography" 100.00 99 97.98 100.00 1.95e-61 PDB 3H5B "Crystal Structure Of Wild Type Hiv-1 Protease With Novel P1'-Ligand Grl-02031" 100.00 99 97.98 100.00 1.95e-61 PDB 3I6O "Crystal Structure Of Wild Type Hiv-1 Protease With Macrocyclic Inhibitor Grl-0216a" 100.00 99 97.98 100.00 1.95e-61 PDB 3JVW "Hiv-1 Protease Mutant G86a With Symmetric Inhibitor Dmp323" 100.00 99 96.97 98.99 6.32e-61 PDB 3JVY "Hiv-1 Protease Mutant G86a With Darunavir" 100.00 99 96.97 98.99 6.32e-61 PDB 3JW2 "Hiv-1 Protease Mutant G86s With Darunavir" 100.00 99 96.97 98.99 6.82e-61 PDB 3K4V "New Crystal Form Of Hiv-1 Protease/saquinavir Structure Reveals Carbamylation Of N-terminal Proline" 100.00 99 97.98 100.00 1.95e-61 PDB 3NDT "Hiv-1 Protease Saquinavir:ritonavir 1:1 Complex Structure" 100.00 100 97.98 100.00 2.01e-61 PDB 3NDU "Hiv-1 Protease Saquinavir:ritonavir 1:5 Complex Structure" 100.00 100 97.98 100.00 2.01e-61 PDB 3NDW "Hiv-1 Protease Saquinavir:ritonavir 1:15 Complex Structure" 100.00 99 97.98 100.00 1.95e-61 PDB 3NDX "Hiv-1 Protease Saquinavir:ritonavir 1:50 Complex Structure" 100.00 99 97.98 100.00 1.95e-61 PDB 3NU3 "Wild Type Hiv-1 Protease With Antiviral Drug Amprenavir" 100.00 99 97.98 100.00 1.95e-61 PDB 3NU4 "Crystal Structure Of Hiv-1 Protease Mutant V32i With Antiviral Drug Amprenavir" 100.00 99 96.97 100.00 3.54e-61 PDB 3NU5 "Crystal Structure Of Hiv-1 Protease Mutant I50v With Antiviral Drug Amprenavir" 100.00 99 96.97 100.00 2.98e-61 PDB 3NU6 "Crystal Structure Of Hiv-1 Protease Mutant I54m With Antiviral Drug Amprenavir" 100.00 99 96.97 100.00 4.22e-61 PDB 3NU9 "Crystal Structure Of Hiv-1 Protease Mutant I84v With Antiviral Drug Amprenavir" 100.00 99 98.99 100.00 1.14e-61 PDB 3NUJ "Crystal Structure Of Hiv-1 Protease Mutant I54v With Antiviral Drug Amprenavir" 100.00 99 96.97 100.00 2.98e-61 PDB 3NUO "Crystal Structure Of Hiv-1 Protease Mutant L90m With Antiviral Drug Amprenavir" 100.00 99 96.97 100.00 3.54e-61 PDB 3OK9 "Crystal Structure Of Wild-Type Hiv-1 Protease With New Oxatricyclic Designed Inhibitor Grl-0519a" 100.00 99 97.98 100.00 1.95e-61 PDB 3OXC "Wild Type Hiv-1 Protease With Antiviral Drug Saquinavir" 100.00 99 97.98 100.00 1.95e-61 PDB 3PWM "Hiv-1 Protease Mutant L76v With Darunavir" 100.00 99 96.97 100.00 6.97e-61 PDB 3PWR "Hiv-1 Protease Mutant L76v Complexed With Saquinavir" 100.00 99 96.97 100.00 6.97e-61 PDB 3QAA "Hiv-1 Wild Type Protease With A Substituted Bis-Tetrahydrofuran Inhibitor, Grl-044-10a" 100.00 99 97.98 100.00 1.95e-61 PDB 3ST5 "Crystal Structure Of Wild-Type Hiv-1 Protease With C3-Substituted Hexahydrocyclopentafuranyl Urethane As P2-Ligand, Grl-0489a" 100.00 99 97.98 100.00 1.95e-61 PDB 3TKG "Crystal Structure Of Hiv Model Protease PrecursorSAQUINAVIR COMPLEX" 100.00 103 97.98 100.00 1.53e-61 PDB 3TKW "Crystal Structure Of Hiv Protease Model PrecursorDARUNAVIR COMPLEX" 100.00 103 97.98 100.00 1.53e-61 PDB 3TL9 "Crystal Structure Of Hiv Protease Model PrecursorSAQUINAVIR COMPLEX" 100.00 103 97.98 100.00 1.53e-61 PDB 3TOF "Hiv-1 Protease - Epoxydic Inhibitor Complex (Ph 6 - Orthorombic Crystal Form P212121)" 100.00 99 97.98 100.00 1.95e-61 PDB 3TOG "Hiv-1 Protease - Epoxydic Inhibitor Complex (ph 9 - Monoclinic Crystal Form P21)" 100.00 99 97.98 100.00 1.95e-61 PDB 3TOH "Hiv-1 Protease - Epoxydic Inhibitor Complex (ph 9 - Orthorombic Crystal Form P212121)" 100.00 99 97.98 100.00 1.95e-61 PDB 3VF5 "Crystal Structure Of Hiv-1 Protease Mutant I47v With Novel P1'-ligands Grl-02031" 100.00 99 96.97 100.00 2.98e-61 PDB 3VF7 "Crystal Structure Of Hiv-1 Protease Mutant L76v With Novel P1'-ligands Grl-02031" 100.00 99 96.97 100.00 6.97e-61 PDB 3VFA "Crystal Structure Of Hiv-1 Protease Mutant V82a With Novel P1'-ligands Grl-02031" 100.00 99 96.97 98.99 6.11e-61 PDB 3VFB "Crystal Structure Of Hiv-1 Protease Mutant N88d With Novel P1'-ligands Grl-02031" 100.00 99 96.97 100.00 1.02e-60 PDB 4DFG "Crystal Structure Of Wild-Type Hiv-1 Protease With Cyclopentyltetrahydro- Furanyl Urethanes As P2-Ligand, Grl-0249a" 100.00 99 97.98 100.00 1.95e-61 PDB 4EJ8 "Apo Hiv Protease (pr) Dimer In Closed Form With Fragment 1f1 In The Outside/top Of Flap" 100.00 99 96.97 100.00 7.77e-61 PDB 4EJL "Apo Hiv Protease (pr) Dimer In Closed Form With Fragment 1f1-n In The Outside/top Of Flap" 100.00 99 96.97 100.00 7.77e-61 PDB 4FL8 "Hiv-1 Protease Complexed With Gem-Diol-Amine Tetrahedral Intermediate" 100.00 99 97.98 100.00 1.95e-61 PDB 4FLG "Hiv-1 Protease Mutant I47v Complexed With Reaction Intermediate" 100.00 99 96.97 100.00 2.98e-61 PDB 4FM6 "Hiv-1 Protease Mutant V32i Complexed With Reaction Intermediate" 100.00 99 96.97 100.00 3.54e-61 PDB 4HDB "Crystal Structure Of Hiv-1 Protease Mutants D30n Complexed With Inhibitor Grl-0519" 100.00 99 96.97 100.00 8.76e-61 PDB 4HDF "Crystal Structure Of Hiv-1 Protease Mutants V82a Complexed With Inhibitor Grl-0519" 100.00 99 96.97 98.99 6.11e-61 PDB 4HDP "Crystal Structure Of Hiv-1 Protease Mutants I50v Complexed With Inhibitor Grl-0519" 100.00 99 96.97 100.00 2.98e-61 PDB 4HE9 "Crystal Structure Of Hiv-1 Protease Mutants I54m Complexed With Inhibitor Grl-0519" 100.00 99 96.97 100.00 4.22e-61 PDB 4HEG "Crystal Structure Of Hiv-1 Protease Mutants R8q Complexed With Inhibitor Grl-0519" 100.00 99 96.97 100.00 9.45e-61 PDB 4KB9 "Crystal Structure Of Wild-type Hiv-1 Protease With Novel Tricyclic P2- Ligands Grl-0739a" 100.00 99 97.98 100.00 1.95e-61 PDB 4U8W "Hiv-1 Wild Type Protease With Grl-050-10a (a Gem-difluoro-bis- Tetrahydrofuran As P2-ligand)" 100.00 99 97.98 100.00 1.95e-61 PDB 4ZIP "Hiv-1 Wild Type Protease With Grl-0648a (a Isophthalamide-derived P2- Ligand)" 100.00 99 97.98 100.00 1.95e-61 PDB 4ZLS "Hiv-1 Wild Type Protease With Grl-096-13a (a Boc-derivative P2-ligand, 3,-5-dimethylbiphenyl P1-ligand)" 100.00 99 97.98 100.00 1.95e-61 PDB 5BRY "Hiv-1 Wild Type Protease With Grl-011-11a (a Methylamine Bis- Tetrahydrofuran P2-ligand, Sulfonamide Isostere Derivate)" 100.00 99 97.98 100.00 1.95e-61 PDB 5BS4 "Hiv-1 Wild Type Protease With Grl-047-11a (a Methylamine Bis- Tetrahydrofuran P2-ligand, 4-amino Sulfonamide Derivative)" 100.00 99 97.98 100.00 1.95e-61 stop_ save_ save_substrate_C _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common substrate_C _Molecular_mass . _Mol_thiol_state 'not present' _Details 'residues 5,9 are Norleucine. residue 6 is nitrophenylalanine' _Residue_count 9 _Mol_residue_sequence KARVXXQAX loop_ _Residue_seq_code _Residue_label 1 LYS 2 ALA 3 ARG 4 VAL 5 NLE 6 PPN 7 GLN 8 ALA 9 NLE stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_HIV-PR(D25N) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common HIV-PR(D25N) _Molecular_mass . _Mol_thiol_state 'not reported' _Details 'HIV-1 protease construct with active site PR' _Residue_count 99 _Mol_residue_sequence ; PQVTLWKRPLVTIKIGGQLK EALLNTGADDTVIEEMSLPG RWKPKMIGGIGGFIKVRQYD QIIIEIAGHKAIGTVLVGPT PVNVIGRNLLTQIGATLNF ; loop_ _Residue_seq_code _Residue_label 1 PRO 2 GLN 3 VAL 4 THR 5 LEU 6 TRP 7 LYS 8 ARG 9 PRO 10 LEU 11 VAL 12 THR 13 ILE 14 LYS 15 ILE 16 GLY 17 GLY 18 GLN 19 LEU 20 LYS 21 GLU 22 ALA 23 LEU 24 LEU 25 ASN 26 THR 27 GLY 28 ALA 29 ASP 30 ASP 31 THR 32 VAL 33 ILE 34 GLU 35 GLU 36 MET 37 SER 38 LEU 39 PRO 40 GLY 41 ARG 42 TRP 43 LYS 44 PRO 45 LYS 46 MET 47 ILE 48 GLY 49 GLY 50 ILE 51 GLY 52 GLY 53 PHE 54 ILE 55 LYS 56 VAL 57 ARG 58 GLN 59 TYR 60 ASP 61 GLN 62 ILE 63 ILE 64 ILE 65 GLU 66 ILE 67 ALA 68 GLY 69 HIS 70 LYS 71 ALA 72 ILE 73 GLY 74 THR 75 VAL 76 LEU 77 VAL 78 GLY 79 PRO 80 THR 81 PRO 82 VAL 83 ASN 84 VAL 85 ILE 86 GLY 87 ARG 88 ASN 89 LEU 90 LEU 91 THR 92 GLN 93 ILE 94 GLY 95 ALA 96 THR 97 LEU 98 ASN 99 PHE stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-30 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 1FGC "Structural Implications Of Drug Resistant Mutants Of Hiv-1 Protease: High Resolution Crystal Structures Of The Mutant ProteaseS" 100.00 99 96.97 100.00 6.32e-61 PDB 1SDT "Crystal Structures Of Hiv Protease V82a And L90m Mutants Reveal Changes In Indinavir Binding Site." 100.00 99 96.97 100.00 6.32e-61 PDB 2A1E "High Resolution Structure Of Hiv-1 Pr With Ts-126" 100.00 99 96.97 100.00 6.32e-61 PDB 2AOC "Crystal Structure Analysis Of Hiv-1 Protease Mutant I84v With A Substrate Analog P2-Nc" 100.00 99 97.98 100.00 3.39e-61 PDB 2AOD "Crystal Structure Analysis Of Hiv-1 Protease With A Substrate Analog P2-Nc" 100.00 99 96.97 100.00 6.32e-61 PDB 2AOI "Crystal Structure Analysis Of Hiv-1 Protease With A Substrate Analog P1-P6" 100.00 99 96.97 100.00 6.32e-61 PDB 2AOJ "Crystal Structure Analysis Of Hiv-1 Protease With A Substrate Analog P6-Pr" 100.00 99 96.97 100.00 6.32e-61 PDB 2HB3 "Wild-Type Hiv-1 Protease In Complex With Potent Inhibitor Grl06579" 100.00 99 96.97 100.00 6.32e-61 PDB 2IEN "Crystal Structure Analysis Of Hiv-1 Protease With A Potent Non-Peptide Inhibitor (Uic-94017)" 100.00 99 96.97 100.00 6.32e-61 PDB 2IEO "Crystal Structure Analysis Of Hiv-1 Protease Mutant I84v With A Potent Non-peptide Inhibitor (uic-94017)" 100.00 99 97.98 100.00 3.39e-61 PDB 2NNK "Crystal Structure Analysis Of Hiv-1 Protease Mutant I84v With A Inhibitor Saquinavir" 100.00 99 97.98 100.00 3.39e-61 PDB 2NNP "Crystal Structure Analysis Of Hiv-1 Protease Mutant I84v With A Inhibitor Saquinavir" 100.00 99 97.98 100.00 3.39e-61 PDB 2QD8 "Hiv-1 Protease Mutant I84v With Potent Antiviral Inhibitor Grl-98065" 100.00 99 97.98 100.00 3.39e-61 PDB 2Z4O "Wild Type Hiv-1 Protease With Potent Antiviral Inhibitor Grl-98065" 100.00 99 96.97 100.00 6.32e-61 PDB 2ZYE "Structure Of Hiv-1 Protease In Complex With Potent Inhibitor Kni-272 Determined By Neutron Crystallography" 98.99 99 96.94 100.00 4.85e-60 PDB 3A2O "Crystal Structure Of Hiv-1 Protease Complexed With Kni-1689" 100.00 99 96.97 100.00 6.32e-61 PDB 3B7V "Hiv-1 Protease Complexed With Gem-Diol-Amine Tetrahedral Intermediate Nlltqi" 100.00 99 96.97 100.00 6.32e-61 PDB 3BVA "Cystal Structure Of Hiv-1 Active Site Mutant D25n And P2-Nc Analog Inhibitor" 100.00 99 97.98 100.00 1.37e-61 PDB 3BVB "Cystal Structure Of Hiv-1 Active Site Mutant D25n And Inhibitor Darunavir" 100.00 99 97.98 100.00 1.37e-61 PDB 3DJK "Wild Type Hiv-1 Protease With Potent Antiviral Inhibitor Grl-0255a" 100.00 99 96.97 100.00 6.32e-61 PDB 3DK1 "Wild Type Hiv-1 Protease With Potent Antiviral Inhibitor Grl-0105a" 100.00 99 96.97 100.00 6.32e-61 PDB 3FX5 "Structure Of Hiv-1 Protease In Complex With Potent Inhibitor Kni-272 Determined By High Resolution X-ray Crystallography" 100.00 99 96.97 100.00 6.32e-61 PDB 3H5B "Crystal Structure Of Wild Type Hiv-1 Protease With Novel P1'-Ligand Grl-02031" 100.00 99 96.97 100.00 6.32e-61 PDB 3I6O "Crystal Structure Of Wild Type Hiv-1 Protease With Macrocyclic Inhibitor Grl-0216a" 100.00 99 96.97 100.00 6.32e-61 PDB 3K4V "New Crystal Form Of Hiv-1 Protease/saquinavir Structure Reveals Carbamylation Of N-terminal Proline" 100.00 99 96.97 100.00 6.32e-61 PDB 3NDT "Hiv-1 Protease Saquinavir:ritonavir 1:1 Complex Structure" 100.00 100 96.97 100.00 6.51e-61 PDB 3NDU "Hiv-1 Protease Saquinavir:ritonavir 1:5 Complex Structure" 100.00 100 96.97 100.00 6.51e-61 PDB 3NDW "Hiv-1 Protease Saquinavir:ritonavir 1:15 Complex Structure" 100.00 99 96.97 100.00 6.32e-61 PDB 3NDX "Hiv-1 Protease Saquinavir:ritonavir 1:50 Complex Structure" 100.00 99 96.97 100.00 6.32e-61 PDB 3NU3 "Wild Type Hiv-1 Protease With Antiviral Drug Amprenavir" 100.00 99 96.97 100.00 6.32e-61 PDB 3NU9 "Crystal Structure Of Hiv-1 Protease Mutant I84v With Antiviral Drug Amprenavir" 100.00 99 97.98 100.00 3.39e-61 PDB 3OK9 "Crystal Structure Of Wild-Type Hiv-1 Protease With New Oxatricyclic Designed Inhibitor Grl-0519a" 100.00 99 96.97 100.00 6.32e-61 PDB 3OXC "Wild Type Hiv-1 Protease With Antiviral Drug Saquinavir" 100.00 99 96.97 100.00 6.32e-61 PDB 3QAA "Hiv-1 Wild Type Protease With A Substituted Bis-Tetrahydrofuran Inhibitor, Grl-044-10a" 100.00 99 96.97 100.00 6.32e-61 PDB 3ST5 "Crystal Structure Of Wild-Type Hiv-1 Protease With C3-Substituted Hexahydrocyclopentafuranyl Urethane As P2-Ligand, Grl-0489a" 100.00 99 96.97 100.00 6.32e-61 PDB 3TKG "Crystal Structure Of Hiv Model Protease PrecursorSAQUINAVIR COMPLEX" 100.00 103 96.97 100.00 5.14e-61 PDB 3TKW "Crystal Structure Of Hiv Protease Model PrecursorDARUNAVIR COMPLEX" 100.00 103 96.97 100.00 5.14e-61 PDB 3TL9 "Crystal Structure Of Hiv Protease Model PrecursorSAQUINAVIR COMPLEX" 100.00 103 96.97 100.00 5.14e-61 PDB 3TOF "Hiv-1 Protease - Epoxydic Inhibitor Complex (Ph 6 - Orthorombic Crystal Form P212121)" 100.00 99 96.97 100.00 6.32e-61 PDB 3TOG "Hiv-1 Protease - Epoxydic Inhibitor Complex (ph 9 - Monoclinic Crystal Form P21)" 100.00 99 96.97 100.00 6.32e-61 PDB 3TOH "Hiv-1 Protease - Epoxydic Inhibitor Complex (ph 9 - Orthorombic Crystal Form P212121)" 100.00 99 96.97 100.00 6.32e-61 PDB 4DFG "Crystal Structure Of Wild-Type Hiv-1 Protease With Cyclopentyltetrahydro- Furanyl Urethanes As P2-Ligand, Grl-0249a" 100.00 99 96.97 100.00 6.32e-61 PDB 4FL8 "Hiv-1 Protease Complexed With Gem-Diol-Amine Tetrahedral Intermediate" 100.00 99 96.97 100.00 6.32e-61 PDB 4KB9 "Crystal Structure Of Wild-type Hiv-1 Protease With Novel Tricyclic P2- Ligands Grl-0739a" 100.00 99 96.97 100.00 6.32e-61 PDB 4U8W "Hiv-1 Wild Type Protease With Grl-050-10a (a Gem-difluoro-bis- Tetrahydrofuran As P2-ligand)" 100.00 99 96.97 100.00 6.32e-61 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_NLE _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common NORLEUCINE _BMRB_code . _PDB_code NLE _Standard_residue_derivative . _Molecular_mass 131.173 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Nov 4 13:19:04 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? CE CE C . 0 . ? H H H . 0 . ? HN2 HN2 H . 0 . ? HA HA H . 0 . ? HXT HXT H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 H . 0 . ? HE1 HE1 H . 0 . ? HE2 HE2 H . 0 . ? HE3 HE3 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N H ? ? SING N HN2 ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD CE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING CE HE1 ? ? SING CE HE2 ? ? SING CE HE3 ? ? stop_ save_ save_chem_comp_PPN _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common PARA-NITROPHENYLALANINE _BMRB_code . _PDB_code PPN _Standard_residue_derivative . _Molecular_mass 210.187 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Nov 4 13:19:44 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD1 CD1 C . 0 . ? CD2 CD2 C . 0 . ? CE1 CE1 C . 0 . ? CE2 CE2 C . 0 . ? CZ CZ C . 0 . ? N1 N1 N . 1 . ? O1 O1 O . 0 . ? O2 O2 O . -1 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HXT HXT H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HD1 HD1 H . 0 . ? HD2 HD2 H . 0 . ? HE1 HE1 H . 0 . ? HE2 HE2 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N H ? ? SING N H2 ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB CG CD1 ? ? SING CG CD2 ? ? SING CD1 CE1 ? ? SING CD1 HD1 ? ? DOUB CD2 CE2 ? ? SING CD2 HD2 ? ? DOUB CE1 CZ ? ? SING CE1 HE1 ? ? SING CE2 CZ ? ? SING CE2 HE2 ? ? SING CZ N1 ? ? DOUB N1 O1 ? ? SING N1 O2 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $HIV-PR HIV 12721 . . HIV HIV stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $HIV-PR 'recombinant technology' . Escherichia coli . na $HIV-PR 'recombinant technology' . Escherichia coli . na stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $HIV-PR 0.2 mM [U-15N] $substrate_C 6 mM 'natural abundance' 'sodium phosphate' 20 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $HIV-PR 0.2 mM [U-15N] $substrate_C 6 mM 'natural abundance' 'sodium phosphate' 20 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_ModelFree _Saveframe_category software _Name ModelFree _Version . loop_ _Vendor _Address _Electronic_address Palmer . . stop_ loop_ _Task 'chemical exchange contribution to T2' 'order parameter identification' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 750 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.8 . pH pressure 1 . atm temperature 293.15 . K stop_ save_