data_16660 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; SOLUTION CONFORMATION OF SUBSTANCE P IN WATER COMPLEXED WITH NK1R ; _BMRB_accession_number 16660 _BMRB_flat_file_name bmr16660.str _Entry_type new _Submission_date 2009-12-31 _Accession_date 2009-12-31 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'This is 5 conformer ensemble structure of Substance P-NK1 complex as obtained running Autodock where the ligand SP was generated from XPLOR-NIH' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gayen Anindita . . 2 Mukhopadhyay Chaitali . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 82 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-03-17 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 20115 'Substance P 40 structures in water pH 5.5 298 K' 20116 'Substance P in DMPC:CHAPS q=0.25 bicelles' 20117 'Substance P in isotropic q=0.25 DMPC/CHAPS/GM1 bicelles' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'NMR evidence of GM1-induced conformational change of Substance P using isotropic bicelles.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20937248 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gayen Anindita . . 2 Goswami 'Sudipto Kishore' . . 3 Mukhopadhyay Chaitali . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_name_full 'Biochimica et biophysica acta' _Journal_volume 1808 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 127 _Page_last 139 _Year 2011 _Details . loop_ _Keyword 'Substance P' NMR NK1 Water stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Substance P-NK1 complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Substance_P $Substance_P NK1R $NK1R 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_Substance_P _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Substance_P _Molecular_mass . _Mol_thiol_state 'not present' loop_ _Biological_function neuromodulator stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence RPKPQQFFGLM loop_ _Residue_seq_code _Residue_label 1 ARG 2 PRO 3 LYS 4 PRO 5 GLN 6 GLN 7 PHE 8 PHE 9 GLY 10 LEU 11 MET stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_NK1R _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common NK1R _Molecular_mass 43012.852 _Mol_thiol_state 'not present' loop_ _Biological_function 'Substance P is a Neuromodulator' stop_ _Details . _Residue_count 375 _Mol_residue_sequence ; MDNVLPVDSDLSPNISTNTS EPNQFVQPAWQIVLWAAAYT VIVVTSVVGNVVVMWIILAH KRMRTVTNYFLVNLAFAEAS MAAFNTVVNFTYAVHNEWYY GLFYCKFHNFFPIAAVFASI YSMTAVAFDRYMAIIHPLQP RLSATATKVVICVIWVLALL LAFPQGYYSTTETMPSRVVC MIEWPEHPNKIYEKVYHICV TVLIYFLPLLVIGYAYTVVG ITLWASEIPGDSSDRYHEQV SAKRKVVKMMIVVVCTFAIC WLPFHIFFLLPYINPDLYLK KFIQQVYLAIMWLAMSSTMY NPIIYCCLNDRFRLGFKHAF RCCPFISAGDYEGLEMKSTR YLQTQGSVYKVSRLETTIST VVGARPKPQQFFGLM ; loop_ _Residue_seq_code _Residue_label 1 MET 2 ASP 3 ASN 4 VAL 5 LEU 6 PRO 7 VAL 8 ASP 9 SER 10 ASP 11 LEU 12 SER 13 PRO 14 ASN 15 ILE 16 SER 17 THR 18 ASN 19 THR 20 SER 21 GLU 22 PRO 23 ASN 24 GLN 25 PHE 26 VAL 27 GLN 28 PRO 29 ALA 30 TRP 31 GLN 32 ILE 33 VAL 34 LEU 35 TRP 36 ALA 37 ALA 38 ALA 39 TYR 40 THR 41 VAL 42 ILE 43 VAL 44 VAL 45 THR 46 SER 47 VAL 48 VAL 49 GLY 50 ASN 51 VAL 52 VAL 53 VAL 54 MET 55 TRP 56 ILE 57 ILE 58 LEU 59 ALA 60 HIS 61 LYS 62 ARG 63 MET 64 ARG 65 THR 66 VAL 67 THR 68 ASN 69 TYR 70 PHE 71 LEU 72 VAL 73 ASN 74 LEU 75 ALA 76 PHE 77 ALA 78 GLU 79 ALA 80 SER 81 MET 82 ALA 83 ALA 84 PHE 85 ASN 86 THR 87 VAL 88 VAL 89 ASN 90 PHE 91 THR 92 TYR 93 ALA 94 VAL 95 HIS 96 ASN 97 GLU 98 TRP 99 TYR 100 TYR 101 GLY 102 LEU 103 PHE 104 TYR 105 CYS 106 LYS 107 PHE 108 HIS 109 ASN 110 PHE 111 PHE 112 PRO 113 ILE 114 ALA 115 ALA 116 VAL 117 PHE 118 ALA 119 SER 120 ILE 121 TYR 122 SER 123 MET 124 THR 125 ALA 126 VAL 127 ALA 128 PHE 129 ASP 130 ARG 131 TYR 132 MET 133 ALA 134 ILE 135 ILE 136 HIS 137 PRO 138 LEU 139 GLN 140 PRO 141 ARG 142 LEU 143 SER 144 ALA 145 THR 146 ALA 147 THR 148 LYS 149 VAL 150 VAL 151 ILE 152 CYS 153 VAL 154 ILE 155 TRP 156 VAL 157 LEU 158 ALA 159 LEU 160 LEU 161 LEU 162 ALA 163 PHE 164 PRO 165 GLN 166 GLY 167 TYR 168 TYR 169 SER 170 THR 171 THR 172 GLU 173 THR 174 MET 175 PRO 176 SER 177 ARG 178 VAL 179 VAL 180 CYS 181 MET 182 ILE 183 GLU 184 TRP 185 PRO 186 GLU 187 HIS 188 PRO 189 ASN 190 LYS 191 ILE 192 TYR 193 GLU 194 LYS 195 VAL 196 TYR 197 HIS 198 ILE 199 CYS 200 VAL 201 THR 202 VAL 203 LEU 204 ILE 205 TYR 206 PHE 207 LEU 208 PRO 209 LEU 210 LEU 211 VAL 212 ILE 213 GLY 214 TYR 215 ALA 216 TYR 217 THR 218 VAL 219 VAL 220 GLY 221 ILE 222 THR 223 LEU 224 TRP 225 ALA 226 SER 227 GLU 228 ILE 229 PRO 230 GLY 231 ASP 232 SER 233 SER 234 ASP 235 ARG 236 TYR 237 HIS 238 GLU 239 GLN 240 VAL 241 SER 242 ALA 243 LYS 244 ARG 245 LYS 246 VAL 247 VAL 248 LYS 249 MET 250 MET 251 ILE 252 VAL 253 VAL 254 VAL 255 CYS 256 THR 257 PHE 258 ALA 259 ILE 260 CYS 261 TRP 262 LEU 263 PRO 264 PHE 265 HIS 266 ILE 267 PHE 268 PHE 269 LEU 270 LEU 271 PRO 272 TYR 273 ILE 274 ASN 275 PRO 276 ASP 277 LEU 278 TYR 279 LEU 280 LYS 281 LYS 282 PHE 283 ILE 284 GLN 285 GLN 286 VAL 287 TYR 288 LEU 289 ALA 290 ILE 291 MET 292 TRP 293 LEU 294 ALA 295 MET 296 SER 297 SER 298 THR 299 MET 300 TYR 301 ASN 302 PRO 303 ILE 304 ILE 305 TYR 306 CYS 307 CYS 308 LEU 309 ASN 310 ASP 311 ARG 312 PHE 313 ARG 314 LEU 315 GLY 316 PHE 317 LYS 318 HIS 319 ALA 320 PHE 321 ARG 322 CYS 323 CYS 324 PRO 325 PHE 326 ILE 327 SER 328 ALA 329 GLY 330 ASP 331 TYR 332 GLU 333 GLY 334 LEU 335 GLU 336 MET 337 LYS 338 SER 339 THR 340 ARG 341 TYR 342 LEU 343 GLN 344 THR 345 GLN 346 GLY 347 SER 348 VAL 349 TYR 350 LYS 351 VAL 352 SER 353 ARG 354 LEU 355 GLU 356 THR 357 THR 358 ILE 359 SER 360 THR 361 VAL 362 VAL 363 GLY 364 ALA 365 ARG 366 PRO 367 LYS 368 PRO 369 GLN 370 GLN 371 PHE 372 PHE 373 GLY 374 LEU 375 MET 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 2KS9 "Solution Conformation Of Substance P In Water Complexed With Nk1r" 97.07 364 100.00 100.00 0.00e+00 PDB 2KSA "Substance P In DmpcCHAPS ISOTROPIC Q0.25 BICELLES AS A LIGAND FOR Nk1r" 97.07 364 100.00 100.00 0.00e+00 PDB 2KSB "Substance P In Isotropic Q0.25 DmpcCHAPSGM1 BICELLES AS A LIGAND For Nk1r" 97.07 364 100.00 100.00 0.00e+00 DBJ BAE53724 "NK-1 receptor [Macaca mulatta]" 98.67 407 98.11 98.65 0.00e+00 DBJ BAF82454 "unnamed protein product [Homo sapiens]" 98.67 407 98.38 98.92 0.00e+00 EMBL CAA46292 "substance P receptor [Homo sapiens]" 98.67 407 98.38 98.92 0.00e+00 EMBL CAI58656 "tachykinin receptor 1 [Canis lupus familiaris]" 97.87 407 97.82 98.91 0.00e+00 GB AAA17891 "substance P, NK-1 receptor, partial [Mus musculus]" 60.53 228 96.92 97.80 2.20e-156 GB AAA17892 "substance P, NK-1 receptor, partial [Mus musculus]" 60.53 228 96.92 97.80 2.20e-156 GB AAA36641 "substance P receptor (long form) [Homo sapiens]" 98.67 407 98.38 98.92 0.00e+00 GB AAA36644 "substance P receptor (short form) [Homo sapiens]" 82.93 311 100.00 100.00 0.00e+00 GB AAA59933 "NK-1 receptor [Homo sapiens]" 98.67 407 98.38 98.92 0.00e+00 REF NP_001012637 "substance-P receptor [Canis lupus familiaris]" 97.87 407 97.82 98.91 0.00e+00 REF NP_001032950 "substance-P receptor [Macaca mulatta]" 98.67 407 98.11 98.65 0.00e+00 REF NP_001049 "substance-P receptor isoform long [Homo sapiens]" 98.67 407 98.38 98.92 0.00e+00 REF NP_001166333 "substance-P receptor isoform short [Cavia porcellus]" 82.93 311 98.71 99.04 0.00e+00 REF NP_056542 "substance-P receptor isoform short [Homo sapiens]" 82.93 311 100.00 100.00 0.00e+00 SP P25103 "RecName: Full=Substance-P receptor; Short=SPR; AltName: Full=NK-1 receptor; Short=NK-1R; AltName: Full=Tachykinin receptor 1 [H" 98.67 407 98.38 98.92 0.00e+00 SP Q5DUB3 "RecName: Full=Substance-P receptor; Short=SPR; AltName: Full=NK-1 receptor; Short=NK-1R; AltName: Full=Tachykinin receptor 1 [C" 97.87 407 97.82 98.91 0.00e+00 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Substance_P . . . . . . $NK1R Human 9606 Eukaryota Metazoa . . 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 $Substance_P 'obtained from a vendor' . . . . . $NK1R 'obtained from a vendor' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_Substance_P _Saveframe_category sample _Sample_type solution _Details 'taken in water of pH 5.5 temp 298K' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Substance_P 3.7 mM 'natural abundance' $NK1R . mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address 'Thomas Goddard' . . stop_ loop_ _Task processing stop_ _Details . save_ save_XPLORNIH _Saveframe_category software _Name XPLORNIH _Version . loop_ _Vendor _Address _Electronic_address 'Charles Schwieters' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_AUTODOCK _Saveframe_category software _Name AUTODOCK _Version . loop_ _Vendor _Address _Electronic_address 'aka olson' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_Substance_P save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_Substance_P save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_Substance_P save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details 'experiment done in water of pH 5.5 298K' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 5.5 . pH pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_TMS_used_as_reference _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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 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 1H-1H TOCSY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_Substance_P stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $TMS_used_as_reference _Mol_system_component_name Substance_P _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 ARG HA H 4.068 . 1 2 1 1 ARG HB2 H 1.824 . . 3 1 1 ARG HB3 H 1.824 . . 4 1 1 ARG HD2 H 3.222 . . 5 1 1 ARG HD3 H 3.222 . . 6 1 1 ARG HG2 H 1.305 . . 7 1 1 ARG HG3 H 1.305 . . 8 2 2 PRO HA H 4.441 . 1 9 2 2 PRO HB2 H 1.865 . . 10 2 2 PRO HB3 H 1.998 . . 11 2 2 PRO HD2 H 3.592 . . 12 2 2 PRO HD3 H 3.749 . . 13 2 2 PRO HG2 H 1.839 . . 14 2 2 PRO HG3 H 1.862 . . 15 3 3 LYS H H 8.478 . 1 16 3 3 LYS HA H 4.452 . 1 17 3 3 LYS HB2 H 1.816 . . 18 3 3 LYS HB3 H 1.816 . . 19 3 3 LYS HD2 H 1.680 . . 20 3 3 LYS HD3 H 1.680 . . 21 3 3 LYS HE2 H 2.982 . . 22 3 3 LYS HE3 H 2.982 . . 23 3 3 LYS HG2 H 1.498 . . 24 3 3 LYS HG3 H 1.498 . . 25 4 4 PRO HA H 4.37 . 1 26 4 4 PRO HB2 H 1.993 . . 27 4 4 PRO HB3 H 2.011 . . 28 4 4 PRO HD2 H 3.632 . . 29 4 4 PRO HD3 H 3.837 . . 30 4 4 PRO HG2 H 1.868 . . 31 4 4 PRO HG3 H 2.313 . . 32 5 5 GLN H H 8.446 . 1 33 5 5 GLN HA H 4.193 . 1 34 5 5 GLN HB2 H 1.939 . . 35 5 5 GLN HB3 H 1.939 . . 36 5 5 GLN HE21 H 6.87 . . 37 5 5 GLN HE22 H 7.516 . . 38 5 5 GLN HG2 H 2.262 . . 39 5 5 GLN HG3 H 2.262 . . 40 6 6 GLN H H 8.244 . 1 41 6 6 GLN HA H 4.217 . 1 42 6 6 GLN HB2 H 1.810 . . 43 6 6 GLN HB3 H 1.810 . . 44 6 6 GLN HE21 H 6.857 . . 45 6 6 GLN HE22 H 7.422 . . 46 6 6 GLN HG2 H 2.128 . . 47 6 6 GLN HG3 H 2.128 . . 48 7 7 PHE H H 8.204 . 1 49 7 7 PHE HA H 4.571 . 1 50 7 7 PHE HB2 H 2.892 . . 51 7 7 PHE HB3 H 3.045 . . 52 7 7 PHE HD1 H 7.189 . . 53 7 7 PHE HD2 H 7.189 . . 54 7 7 PHE HE1 H 7.295 . . 55 7 7 PHE HE2 H 7.295 . . 56 7 7 PHE HZ H 7.255 . 1 57 8 8 PHE H H 8.198 . 1 58 8 8 PHE HA H 4.588 . 1 59 8 8 PHE HB2 H 2.920 . . 60 8 8 PHE HB3 H 3.154 . . 61 8 8 PHE HD1 H 7.246 . . 62 8 8 PHE HD2 H 7.246 . . 63 8 8 PHE HE1 H 7.336 . . 64 8 8 PHE HE2 H 7.336 . . 65 8 8 PHE HZ H 7.31 . 1 66 9 9 GLY H H 7.862 . 1 67 9 9 GLY HA2 H 3.852 . . 68 9 9 GLY HA3 H 3.852 . . 69 10 10 LEU H H 8.120 . 1 70 10 10 LEU HA H 4.315 . 1 71 10 10 LEU HB2 H 1.613 . . 72 10 10 LEU HB3 H 1.613 . . 73 10 10 LEU HD1 H 0.935 . . 74 10 10 LEU HD2 H 0.887 . . 75 10 10 LEU HG H 1.613 . 1 76 11 11 MET H H 8.329 . 1 77 11 11 MET HA H 4.445 . 1 78 11 11 MET HB2 H 2.005 . . 79 11 11 MET HB3 H 2.070 . . 80 11 11 MET HE H 7.096 . 1 81 11 11 MET HG2 H 2.490 . . 82 11 11 MET HG3 H 2.605 . . stop_ save_