BMRB Entry 16660

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR16660
MolProbity Validation Chart

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Title:
SOLUTION CONFORMATION OF SUBSTANCE P IN WATER COMPLEXED WITH NK1R
Deposition date:
2009-12-31
Original release date:
2011-03-17
Authors:
Gayen, Anindita; Mukhopadhyay, Chaitali
Citation:

Citation: Gayen, Anindita; Goswami, Sudipto Kishore; Mukhopadhyay, Chaitali. "NMR evidence of GM1-induced conformational change of Substance P using isotropic bicelles."  Biochim. Biophys. Acta 1808, 127-139 (2011).
PubMed: 20937248

Assembly members:

Assembly members:
Substance_P, polymer, 11 residues, Formula weight is not available
NK1R, polymer, 375 residues, 43012.852 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:

Experimental source:   Production method: obtained from a vendor   Host organism: synthesized

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Substance_P: RPKPQQFFGLM
NK1R: MDNVLPVDSDLSPNISTNTS EPNQFVQPAWQIVLWAAAYT VIVVTSVVGNVVVMWIILAH KRMRTVTNYFLVNLAFAEAS MAAFNTVVNFTYAVHNEWYY GLFYCKFHNFFPIAAVFASI YSMTAVAFDRYMAIIHPLQP RLSATATKVVICVIWVLALL LAFPQGYYSTTETMPSRVVC MIEWPEHPNKIYEKVYHICV TVLIYFLPLLVIGYAYTVVG ITLWASEIPGDSSDRYHEQV SAKRKVVKMMIVVVCTFAIC WLPFHIFFLLPYINPDLYLK KFIQQVYLAIMWLAMSSTMY NPIIYCCLNDRFRLGFKHAF RCCPFISAGDYEGLEMKSTR YLQTQGSVYKVSRLETTIST VVGARPKPQQFFGLM

Data sets:
Data typeCount
1H chemical shifts88

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Substance_P1
2NK1R2

Entities:

Entity 1, Substance_P 11 residues - Formula weight is not available

1   ARGPROLYSPROGLNGLNPHEPHEGLYLEU
2   MET

Entity 2, NK1R 375 residues - 43012.852 Da.

1   METASPASNVALLEUPROVALASPSERASP
2   LEUSERPROASNILESERTHRASNTHRSER
3   GLUPROASNGLNPHEVALGLNPROALATRP
4   GLNILEVALLEUTRPALAALAALATYRTHR
5   VALILEVALVALTHRSERVALVALGLYASN
6   VALVALVALMETTRPILEILELEUALAHIS
7   LYSARGMETARGTHRVALTHRASNTYRPHE
8   LEUVALASNLEUALAPHEALAGLUALASER
9   METALAALAPHEASNTHRVALVALASNPHE
10   THRTYRALAVALHISASNGLUTRPTYRTYR
11   GLYLEUPHETYRCYSLYSPHEHISASNPHE
12   PHEPROILEALAALAVALPHEALASERILE
13   TYRSERMETTHRALAVALALAPHEASPARG
14   TYRMETALAILEILEHISPROLEUGLNPRO
15   ARGLEUSERALATHRALATHRLYSVALVAL
16   ILECYSVALILETRPVALLEUALALEULEU
17   LEUALAPHEPROGLNGLYTYRTYRSERTHR
18   THRGLUTHRMETPROSERARGVALVALCYS
19   METILEGLUTRPPROGLUHISPROASNLYS
20   ILETYRGLULYSVALTYRHISILECYSVAL
21   THRVALLEUILETYRPHELEUPROLEULEU
22   VALILEGLYTYRALATYRTHRVALVALGLY
23   ILETHRLEUTRPALASERGLUILEPROGLY
24   ASPSERSERASPARGTYRHISGLUGLNVAL
25   SERALALYSARGLYSVALVALLYSMETMET
26   ILEVALVALVALCYSTHRPHEALAILECYS
27   TRPLEUPROPHEHISILEPHEPHELEULEU
28   PROTYRILEASNPROASPLEUTYRLEULYS
29   LYSPHEILEGLNGLNVALTYRLEUALAILE
30   METTRPLEUALAMETSERSERTHRMETTYR
31   ASNPROILEILETYRCYSCYSLEUASNASP
32   ARGPHEARGLEUGLYPHELYSHISALAPHE
33   ARGCYSCYSPROPHEILESERALAGLYASP
34   TYRGLUGLYLEUGLUMETLYSSERTHRARG
35   TYRLEUGLNTHRGLNGLYSERVALTYRLYS
36   VALSERARGLEUGLUTHRTHRILESERTHR
37   VALVALGLYALAARGPROLYSPROGLNGLN
38   PHEPHEGLYLEUMET

Samples:

sample_Substance_P: Substance P 3.7 mM; NK1R mM

sample_conditions_1: pH: 5.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H TOCSYsample_Substance_Pisotropicsample_conditions_1
2D 1H-1H NOESYsample_Substance_Pisotropicsample_conditions_1
2D DQF-COSYsample_Substance_Pisotropicsample_conditions_1

Software:

SPARKY, Thomas Goddard - processing

X-PLOR NIH, Charles Schwieters - structure solution

AUTODOCK, aka olson - geometry optimization

NMR spectrometers:

  • Bruker DRX 500 MHz

Related Database Links:

PDB
DBJ BAE53724 BAF82454
EMBL CAA46292 CAI58656
GB AAA17891 AAA17892 AAA36641 AAA36644 AAA59933
REF NP_001012637 NP_001032950 NP_001049 NP_001166333 NP_056542
SP P25103 Q5DUB3
AlphaFold P25103 Q5DUB3