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_