MolNFT v1 · #184709 · protein

Human neurokinin 1 receptor (NK1R) substance P gs complex

7P02 · Antibody fragment SCFV16: “Human neurokinin 1 receptor (NK1R) substance P gs complex”. Electron microscopy, 2 ligands (CLR, NH2), 12 pockets (best druggability 0.82). MolNFT v1 #184709 on GenesisL1: 3D structure, binding sites and…

PDB: 7P02
Type: protein
Length: 1,138 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody fragment SCFV16; Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit…
UniProt: P62873, P59768, P63096, P63092, P25103, P20366
Ligands: CLR, NH2
Pockets: 12 · best druggability 0.82

Structure

electron microscopy · 6 distinct chains · 35% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Antibody fragment SCFV16	protein	232	5% helix, 47% strand	—
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	333	8% helix, 48% strand	P62873
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	51	51% helix, 0% strand	P59768
A	Guanine nucleotide-binding protein G(I) subunit alpha-1, guanine nucleotide-binding protein G(S) subunit alpha isoforms short	protein	226	48% helix, 13% strand	P63096, P63092
R	Substance-P receptor	protein	287	78% helix, 3% strand	P25103
P	Protachykinin-1	protein	9	0% helix, 0% strand	P20366

Ligands and binding sites

CLR · Cholesterol · ligand · chains R
NH2 · Amino group · ion · chains R, P

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	692	0.82	0.86	55	empty
2	974	0.72	0.76	58	empty
3	158	0.60	0.83	28	empty
4	243	0.57	0.79	39	empty
5	209	0.56	0.79	30	empty

Interfaces

7 interfaces between chains.

B–G · 2004 Å² buried · 18 hydrogen bonds · protein-protein
B–A · 1278 Å² buried · 10 hydrogen bonds · protein-protein
A–R · 1145 Å² buried · 14 hydrogen bonds · protein-protein
R–P · 847 Å² buried · 15 hydrogen bonds · protein-protein
H–A · 588 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7P02 · Human Neurokinin 1 receptor (NK1R) substance P Gs complex · the same entry in another collection · chain P against P, TM-score 1.00
P62873 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 1.00
P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.97
P25103 · AlphaFold monomer V2.0 prediction for substance-P receptor (P25103) · a predicted model of the same protein · chain R against A, TM-score 0.93
P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.73
P20366 · AlphaFold monomer V2.0 prediction for protachykinin-1 (P20366) · a predicted model of the same protein · chain P against A, TM-score 0.47

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P62873
Every structure of UniProt P59768
Every structure of UniProt P63096
Every structure of UniProt P63092
Every structure of UniProt P25103
Every structure of UniProt P20366
Elsewhere: RCSB PDB 7P02 · PDBe 7P02 · UniProt P62873 · UniProt P59768 · UniProt P63096 · UniProt P63092 · UniProt P25103 · UniProt P20366

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