data_15973 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; HGF-binding peptide-10 ; _BMRB_accession_number 15973 _BMRB_flat_file_name bmr15973.str _Entry_type new _Submission_date 2008-10-05 _Accession_date 2008-10-05 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'HGF-binding peptide obtained from phage display library' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Skelton Nicholas J. . 2 Runyon Steven T. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 88 "13C chemical shifts" 56 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-05-27 update BMRB 'update entity/assembly name' 2009-03-04 update BMRB 'complete entry citation' 2008-11-11 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Noncompetitive inhibition of Hepatocyte Growth Factor Dependent Met signaling by a phage-derived peptide' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18973760 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tam Eric M. . 2 Runyon Steven T. . 3 Santell Lydia . . 4 Quan CLiff . . 5 Yao Xiaoyi . . 6 Kirchhofer Daniel . . 7 Skelton Nicholas J. . 8 Lazarus Robert A. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 385 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 79 _Page_last 90 _Year 2009 _Details . loop_ _Keyword 'HGF-binding agtagonist' Met 'Phage display' 'Receptor tyrosine kinase' cancer stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'HGF-binding peptide-10' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'HGF-binding peptide-10' $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'HGF-binding peptide-10' _Molecular_mass 1812.109 _Mol_thiol_state 'all disulfide bound' loop_ _Biological_function 'protein binding' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence VNWVCFRDVGCDWVL loop_ _Residue_seq_code _Residue_label 1 VAL 2 ASN 3 TRP 4 VAL 5 CYS 6 PHE 7 ARG 8 ASP 9 VAL 10 GLY 11 CYS 12 ASP 13 TRP 14 VAL 15 LEU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ######################################## # Molecular bond linkage definitions # ######################################## save_crosslink_bonds _Saveframe_category crosslink_bonds loop_ _Bond_order _Bond_type _Atom_one_mol_system_component_name _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_atom_name _Atom_two_mol_system_component_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_atom_name single disulfide 'HGF-binding peptide-10' 5 CYS SG 'HGF-binding peptide-10' 11 CYS SG stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $entity . . . . . . 'Peptide sequence obtained from synthetic library' 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 $entity 'chemical synthesis' . . . . . 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 'sodium chloride' 25 mM 'natural abundance' D2O 5500 mM '[U-99% 2H]' 'sodium azide' 1 mM 'natural abundance' '1-4 dioxane' 1 mM 'natural abundance' $entity . mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details 'D2O sample' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling 'sodium chloride' 25 mM 'natural abundance' D2O 55000 mM '[U-99% 2H]' 'sodium azide' 1 mM 'natural abundance' $entity . mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_TALOS _Saveframe_category software _Name TALOS _Version . loop_ _Vendor _Address _Electronic_address 'Cornilescu, Delaglio and Bax' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-1H_COSY-35_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY-35' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C 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 temperature 298 . K pH 6.4 . pH pressure 1 . atm 'ionic strength' 0.1 . M stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio dioxane H 1 'methylene protons' ppm 3.75 internal direct . . . 1 dioxane C 13 'methylene protons' ppm 75.0 internal direct . . . 1 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label '2D DQF-COSY' '2D 1H-1H TOCSY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'HGF-binding peptide-10' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 VAL HA H 4.000 0.01 1 2 1 1 VAL HB H 2.052 0.01 1 3 1 1 VAL HG1 H 0.790 0.01 . 4 1 1 VAL HG2 H 0.820 0.01 . 5 1 1 VAL CA C 58.192 0.2 1 6 1 1 VAL CB C 30.850 0.2 1 7 1 1 VAL CG1 C 17.433 0.2 2 8 1 1 VAL CG2 C 18.220 0.2 2 9 2 2 ASN H H 7.137 0.01 1 10 2 2 ASN HA H 5.077 0.01 1 11 2 2 ASN HB2 H 2.583 0.01 . 12 2 2 ASN HB3 H 2.583 0.01 . 13 2 2 ASN HD21 H 7.541 0.01 2 14 2 2 ASN HD22 H 6.845 0.01 2 15 2 2 ASN CA C 50.039 0.2 1 16 2 2 ASN CB C 38.600 0.2 1 17 3 3 TRP H H 8.538 0.01 1 18 3 3 TRP HA H 4.523 0.01 1 19 3 3 TRP HB2 H 2.320 0.01 . 20 3 3 TRP HB3 H 2.875 0.01 2 21 3 3 TRP HD1 H 6.765 0.01 1 22 3 3 TRP HE1 H 9.754 0.01 1 23 3 3 TRP HE3 H 5.769 0.01 1 24 3 3 TRP HH2 H 6.856 0.01 1 25 3 3 TRP HZ2 H 7.105 0.01 1 26 3 3 TRP HZ3 H 6.380 0.01 1 27 3 3 TRP CA C 53.668 0.2 1 28 3 3 TRP CB C 26.677 0.2 1 29 3 3 TRP CD1 C 124.082 0.2 1 30 3 3 TRP CE3 C 117.629 0.2 1 31 3 3 TRP CH2 C 121.476 0.2 1 32 3 3 TRP CZ2 C 111.621 0.2 1 33 3 3 TRP CZ3 C 118.480 0.2 1 34 4 4 VAL H H 8.162 0.01 1 35 4 4 VAL HA H 3.925 0.01 1 36 4 4 VAL HB H 1.590 0.01 1 37 4 4 VAL HG1 H 0.644 0.01 . 38 4 4 VAL HG2 H 0.439 0.01 . 39 4 4 VAL CA C 58.544 0.2 1 40 4 4 VAL CB C 31.896 0.2 1 41 4 4 VAL CG1 C 18.507 0.2 2 42 4 4 VAL CG2 C 18.655 0.2 2 43 5 5 CYS H H 8.086 0.01 1 44 5 5 CYS HA H 4.588 0.01 1 45 5 5 CYS HB2 H 2.592 0.01 . 46 5 5 CYS HB3 H 2.592 0.01 . 47 5 5 CYS CA C 52.125 0.2 1 48 5 5 CYS CB C 42.385 0.2 1 49 6 6 PHE H H 8.249 0.01 1 50 6 6 PHE HA H 4.605 0.01 1 51 6 6 PHE HB2 H 3.070 0.01 . 52 6 6 PHE HB3 H 2.686 0.01 2 53 6 6 PHE HD1 H 7.090 0.01 . 54 6 6 PHE HD2 H 7.090 0.01 . 55 6 6 PHE HE1 H 6.860 0.01 . 56 6 6 PHE HE2 H 6.860 0.01 . 57 6 6 PHE HZ H 6.380 0.01 1 58 6 6 PHE CA C 53.930 0.2 1 59 6 6 PHE CB C 38.201 0.2 1 60 6 6 PHE CD1 C 129.144 0.2 . 61 6 6 PHE CD2 C 129.144 0.2 . 62 6 6 PHE CE1 C 128.605 0.2 . 63 6 6 PHE CE2 C 128.605 0.2 . 64 6 6 PHE CZ C 127.143 0.2 1 65 7 7 ARG H H 7.090 0.01 1 66 7 7 ARG HA H 3.869 0.01 1 67 7 7 ARG HB2 H 1.650 0.01 . 68 7 7 ARG HB3 H 1.650 0.01 . 69 7 7 ARG HD2 H 3.030 0.01 . 70 7 7 ARG HD3 H 3.030 0.01 . 71 7 7 ARG HG2 H 1.403 0.01 . 72 7 7 ARG HG3 H 1.403 0.01 . 73 7 7 ARG CA C 55.083 0.2 1 74 7 7 ARG CB C 27.344 0.2 1 75 7 7 ARG CD C 40.500 0.2 1 76 7 7 ARG CG C 24.105 0.2 1 77 8 8 ASP H H 8.615 0.01 1 78 8 8 ASP HA H 4.310 0.01 1 79 8 8 ASP HB2 H 2.690 0.01 . 80 8 8 ASP HB3 H 2.760 0.01 2 81 8 8 ASP CA C 53.550 0.2 1 82 8 8 ASP CB C 37.401 0.2 1 83 9 9 VAL H H 7.801 0.01 1 84 9 9 VAL HA H 4.119 0.01 1 85 9 9 VAL HB H 2.050 0.01 1 86 9 9 VAL HG1 H 0.790 0.01 . 87 9 9 VAL HG2 H 0.784 0.01 . 88 9 9 VAL CA C 59.984 0.2 1 89 9 9 VAL CB C 30.350 0.2 1 90 9 9 VAL CG1 C 16.973 0.2 2 91 9 9 VAL CG2 C 17.950 0.2 2 92 10 10 GLY H H 7.875 0.01 1 93 10 10 GLY HA2 H 4.196 0.01 . 94 10 10 GLY HA3 H 3.702 0.01 2 95 10 10 GLY CA C 41.802 0.2 1 96 11 11 CYS H H 8.204 0.01 1 97 11 11 CYS HA H 4.948 0.01 1 98 11 11 CYS HB2 H 1.565 0.01 . 99 11 11 CYS HB3 H 2.540 0.01 2 100 11 11 CYS CA C 52.573 0.2 1 101 12 12 ASP H H 8.049 0.01 1 102 12 12 ASP HA H 4.180 0.01 1 103 12 12 ASP HB2 H 2.365 0.01 . 104 12 12 ASP HB3 H 2.365 0.01 . 105 12 12 ASP CA C 50.343 0.2 1 106 12 12 ASP CB C 40.437 0.2 1 107 13 13 TRP H H 8.434 0.01 1 108 13 13 TRP HA H 4.980 0.01 1 109 13 13 TRP HB2 H 2.984 0.01 . 110 13 13 TRP HB3 H 2.984 0.01 . 111 13 13 TRP HD1 H 7.301 0.01 1 112 13 13 TRP HE1 H 10.013 0.01 1 113 13 13 TRP HE3 H 7.343 0.01 1 114 13 13 TRP HH2 H 7.002 0.01 1 115 13 13 TRP HZ2 H 7.161 0.01 1 116 13 13 TRP HZ3 H 7.030 0.01 1 117 13 13 TRP CA C 53.564 0.2 1 118 13 13 TRP CB C 27.460 0.2 1 119 13 13 TRP CD1 C 124.884 0.2 1 120 13 13 TRP CE3 C 117.848 0.2 1 121 13 13 TRP CH2 C 121.768 0.2 1 122 13 13 TRP CZ2 C 112.215 0.2 1 123 13 13 TRP CZ3 C 119.419 0.2 1 124 14 14 VAL H H 8.812 0.01 1 125 14 14 VAL HA H 4.235 0.01 1 126 14 14 VAL HB H 1.960 0.01 1 127 14 14 VAL HG1 H 0.840 0.01 . 128 14 14 VAL HG2 H 0.785 0.01 . 129 14 14 VAL CA C 58.677 0.2 1 130 14 14 VAL CB C 31.494 0.2 1 131 14 14 VAL CG1 C 18.260 0.2 2 132 14 14 VAL CG2 C 18.510 0.2 2 133 15 15 LEU H H 8.036 0.01 1 134 15 15 LEU HA H 4.035 0.01 1 135 15 15 LEU HB2 H 1.494 0.01 . 136 15 15 LEU HB3 H 1.494 0.01 . 137 15 15 LEU HD1 H 0.849 0.01 . 138 15 15 LEU HD2 H 0.802 0.01 . 139 15 15 LEU HG H 1.558 0.01 1 140 15 15 LEU CA C 54.752 0.2 1 141 15 15 LEU CB C 40.222 0.2 1 142 15 15 LEU CD1 C 22.337 0.2 2 143 15 15 LEU CD2 C 21.132 0.2 2 144 15 15 LEU CG C 24.800 0.2 1 stop_ save_