MolNFT v1 · #161736 · protein
Rhodopsin-gi protein complex
6QNO · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Rhodopsin-gi protein complex”. Electron microscopy, 2 ligands (RET, NAG), 17 pockets (best druggability 0.84). MolNFT v1 #161736 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6QNO
- Type
- protein
- Length
- 1,332 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P62871, P02698, P02699
- Ligands
- RET, NAG
- Pockets
- 17 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 212 | 33% helix, 8% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 312 | 1% helix, 46% strand | P62871 |
| G | Guanine nucleotide-binding protein G(T) subunit gamma-T1 | protein | 36 | 50% helix, 0% strand | P02698 |
| L | Fab antibody fragment light chain | protein | 217 | 5% helix, 43% strand | — |
| H | Fab antibody fragment heavy chain | protein | 221 | 5% helix, 51% strand | — |
| R | Rhodopsin | protein | 334 | 67% helix, 3% strand | P02699 |
Ligands and binding sites
- RET · Retinal · ligand · chains R
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.84 | 0.87 | 88 | RET |
| 2 | 746 | 0.84 | 0.87 | 62 | empty |
| 3 | 658 | 0.71 | 0.79 | 87 | empty |
| 4 | 640 | 0.69 | 0.77 | 66 | empty |
| 5 | 241 | 0.68 | 0.84 | 41 | empty |
Interfaces
8 interfaces between chains.
- L–H · 1800 Ų buried · 10 hydrogen bonds · protein-protein
- B–G · 1338 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1131 Ų buried · 9 hydrogen bonds · protein-protein
- A–R · 1131 Ų buried · 13 hydrogen bonds · protein-protein
- B–H · 381 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 cofactor, 1 glycan (disulfide, retinal Schiff base, N-glycosylation).
Compared structures
- 6QNO · Rhodopsin-Gi protein complex · the same entry in another collection · chain R against R, TM-score 1.00
- P62871 · 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 0.97
- 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 0.72
- P02698 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(T) subunit… · a predicted model of the same protein · chain G against A, TM-score 0.71
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 P63096
- Every structure of UniProt P62871
- Every structure of UniProt P02698
- Every structure of UniProt P02699
- Elsewhere: RCSB PDB 6QNO · PDBe 6QNO · UniProt P63096 · UniProt P62871 · UniProt P02698 · UniProt P02699
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