MolNFT v1 · #186693 · protein
Substance P bound to active human neurokinin 1 receptor in complex with MINIGS/Q70
7RMG · Guanine nucleotide-binding protein G(S) subunit alpha…: “Substance P bound to active human neurokinin 1 receptor in complex with MINIGS/Q70”. Electron microscopy, 1 ligand (NH2), 10 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 7RMG
- Type
- protein
- Length
- 968 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(S) subunit alpha isoforms short, with certain…
- UniProt
- P63092, P25103, P20366, P62873, P59768
- Ligands
- NH2
- Pockets
- 10 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short, with certain residues mutated to match guanine nucleotide-binding protein G(Q) subunit | protein | 193 | 40% helix, 21% strand | P63092 |
| R | Substance-P receptor | protein | 289 | 78% helix, 4% strand | P25103 |
| S | Substance P | protein | 11 | 0% helix, 0% strand | P20366 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 322 | 4% helix, 49% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 38 | 63% helix, 0% strand | P59768 |
| N | Nanobody 35 | protein | 115 | 3% helix, 44% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · chains R, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.85 | 0.86 | 119 | empty |
| 2 | 306 | 0.72 | 0.85 | 29 | empty |
| 3 | 97 | 0.64 | 0.89 | 21 | empty |
| 4 | 561 | 0.61 | 0.74 | 46 | empty |
| 5 | 355 | 0.59 | 0.76 | 49 | empty |
Interfaces
6 interfaces between chains.
- B–G · 1426 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1135 Ų buried · 12 hydrogen bonds · protein-protein
- A–R · 931 Ų buried · 7 hydrogen bonds · protein-protein
- R–S · 855 Ų buried · 13 hydrogen bonds · protein-protein
- A–N · 596 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7RMG · Substance P bound to active human neurokinin 1 receptor in complex with miniGs/q70 · the same entry in another collection · chain N against N, 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 0.99
- 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 0.93
- 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
- P20366 · AlphaFold monomer V2.0 prediction for protachykinin-1 (P20366) · a predicted model of the same protein · chain S against A, TM-score 0.29
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 P63092
- Every structure of UniProt P25103
- Every structure of UniProt P20366
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7RMG · PDBe 7RMG · UniProt P63092 · UniProt P25103 · UniProt P20366 · UniProt P62873 · UniProt P59768
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