Research workbench
Structure of the rhodopsin-transducin complex
Analyse Structure of the rhodopsin-transducin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OY9
- Type
- protein
- Length
- 948 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gt-ALPHA/GI1-alpha chimera; Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit…
- UniProt
- P04695, P62871, P02698, P02699
- Ligands
- RET
- Pockets
- 11 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gt-ALPHA/GI1-alpha chimera | protein | 223 | 37% helix, 8% strand | P04695 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 7% helix, 39% strand | P62871 |
| G | Guanine nucleotide-binding protein G(T) subunit gamma-T1 | protein | 60 | 55% helix, 0% strand | P02698 |
| R | Rhodopsin | protein | 326 | 61% helix, 2% strand | P02699 |
Ligands and binding sites
- RET · Retinal · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.83 | 0.89 | 58 | RET |
| 2 | 885 | 0.81 | 0.84 | 79 | empty |
| 3 | 696 | 0.68 | 0.76 | 58 | empty |
| 4 | 65 | 0.48 | 0.84 | 16 | empty |
| 5 | 81 | 0.42 | 0.79 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–G · 2418 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1203 Ų buried · 3 hydrogen bonds · protein-protein
- A–R · 1145 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor, 1 disulfide (retinal Schiff base, disulfide).
Compared structures
- 6OY9 · Structure of the Rhodopsin-Transducin Complex · the same entry in another collection · chain A against A, 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
- P04695 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(T) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.83
- 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 0.78
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 P04695
- Every structure of UniProt P62871
- Every structure of UniProt P02698
- Every structure of UniProt P02699
- Elsewhere: RCSB PDB 6OY9 · PDBe 6OY9 · UniProt P04695 · UniProt P62871 · UniProt P02698 · UniProt P02699
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