MolNFT v1 · #184707 · protein
Human neurokinin 1 receptor (NK1R) substance P gq chimera (mgsqi) complex
7P00 · Antibody fragment SCFV16: “Human neurokinin 1 receptor (NK1R) substance P gq chimera (mgsqi) complex”. Electron microscopy, 2 ligands (CLR, NH2), 9 pockets (best druggability 0.82). MolNFT v1 #184707 on GenesisL1: 3D structure…
- PDB
- 7P00
- Type
- protein
- Length
- 1,144 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, A0A590UJY2, P25103
- Ligands
- CLR, NH2
- Pockets
- 9 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody fragment SCFV16 | protein | 232 | 4% helix, 46% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 333 | 6% helix, 45% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 52 | 50% 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 | 228 | 48% helix, 13% strand | P63096, A0A590UJY2 |
| R | Substance-P receptor | protein | 288 | 79% helix, 3% strand | P25103 |
| P | Substance P | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.82 | 0.85 | 55 | empty |
| 2 | 976 | 0.75 | 0.78 | 77 | empty |
| 3 | 240 | 0.66 | 0.83 | 29 | empty |
| 4 | 261 | 0.57 | 0.78 | 39 | empty |
| 5 | 99 | 0.53 | 0.83 | 28 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2046 Ų buried · 20 hydrogen bonds · protein-protein
- B–A · 1293 Ų buried · 11 hydrogen bonds · protein-protein
- A–R · 1141 Ų buried · 12 hydrogen bonds · protein-protein
- R–P · 896 Ų buried · 10 hydrogen bonds · protein-protein
- H–A · 583 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7P00 · Human Neurokinin 1 receptor (NK1R) substance P Gq chimera (mGsqi) 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 0.96
- P25103 · AlphaFold monomer V2.0 prediction for substance-P receptor (P25103) · a predicted model of the same protein · chain R against A, TM-score 0.92
- 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 0.74
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 A0A590UJY2
- Every structure of UniProt P25103
- Elsewhere: RCSB PDB 7P00 · PDBe 7P00 · UniProt P62873 · UniProt P59768 · UniProt P63096 · UniProt A0A590UJY2 · UniProt P25103
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