Research workbench
Structure of the rhodopsin-transducin-nanobody complex
Analyse Structure of the rhodopsin-transducin-nanobody complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OYA
- Type
- protein
- Length
- 1,056 residues
- Chains
- 5
- 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
- 13 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gt-ALPHA/GI1-alpha chimera | protein | 205 | 38% helix, 14% strand | P04695 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 337 | 7% helix, 35% strand | P62871 |
| G | Guanine nucleotide-binding protein G(T) subunit gamma-T1 | protein | 60 | 42% helix, 0% strand | P02698 |
| N | Camelid antibody vhh fragment | protein | 128 | 0% helix, 40% strand | — |
| R | Rhodopsin | protein | 326 | 66% 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
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.83 | 0.95 | 28 | RET |
| 2 | 784 | 0.83 | 0.86 | 76 | empty |
| 3 | 798 | 0.73 | 0.78 | 56 | empty |
| 4 | 629 | 0.68 | 0.77 | 57 | empty |
| 5 | 79 | 0.62 | 0.90 | 18 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2379 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1319 Ų buried · 8 hydrogen bonds · protein-protein
- A–R · 1112 Ų buried · 14 hydrogen bonds · protein-protein
- A–N · 958 Ų buried · 6 hydrogen bonds · protein-protein
- B–N · 517 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 cofactor (disulfide, retinal Schiff base).
Compared structures
- 6OYA · Structure of the Rhodopsin-Transducin-Nanobody 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 0.99
- 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 0.81
- 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 0.80
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 6OYA · PDBe 6OYA · UniProt P04695 · UniProt P62871 · UniProt P02698 · UniProt P02699
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