Research workbench
SP6-11 biased agonist bound to active human neurokinin 1 receptor in complex with MINIGS/Q70
Analyse SP6-11 biased agonist bound to active human neurokinin 1 receptor in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RMI
- Type
- protein
- Length
- 960 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, P62873, P59768
- Ligands
- NH2
- Pockets
- 14 · best druggability 0.81
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 | 194 | 41% helix, 21% strand | P63092 |
| R | Substance-P receptor | protein | 285 | 78% helix, 4% strand | P25103 |
| S | Substance P 6-11 | protein | 6 | 0% helix, 0% strand | — |
| 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 | 61% helix, 0% strand | P59768 |
| N | Nanobody 35 | protein | 115 | 5% helix, 42% 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
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.81 | 0.85 | 62 | empty |
| 2 | 119 | 0.75 | 0.94 | 31 | empty |
| 3 | 771 | 0.71 | 0.77 | 62 | empty |
| 4 | 398 | 0.67 | 0.80 | 54 | empty |
| 5 | 275 | 0.65 | 0.81 | 24 | empty |
Interfaces
6 interfaces between chains.
- B–G · 1401 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 1120 Ų buried · 11 hydrogen bonds · protein-protein
- A–R · 1031 Ų buried · 5 hydrogen bonds · protein-protein
- A–N · 703 Ų buried · 9 hydrogen bonds · protein-protein
- R–S · 678 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7RMI · SP6-11 biased agonist bound to active human neurokinin 1 receptor in complex with… · 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
- 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
- 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 0.89
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 P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7RMI · PDBe 7RMI · UniProt P63092 · UniProt P25103 · UniProt P62873 · UniProt P59768
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