MolNFT v1 · #149235 · protein
Crystal structure of the rhodopsin-mini-go complex
6FUF: “Crystal structure of the rhodopsin-mini-go complex”. X-ray diffraction, 2 ligands (RET, NAG), 6 pockets (best druggability 0.84). MolNFT v1 #149235 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6FUF
- Type
- protein
- Length
- 497 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin; Guanine nucleotide-binding protein G(O) subunit alpha
- UniProt
- P02699, P09471
- Ligands
- RET, NAG
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin | protein | 316 | 68% helix, 4% strand | P02699 |
| B | Guanine nucleotide-binding protein G(O) subunit alpha | protein | 181 | 36% helix, 20% strand | P09471 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.84 | 0.95 | 33 | RET |
| 2 | 405 | 0.59 | 0.75 | 39 | empty |
| 3 | 157 | 0.58 | 0.82 | 21 | empty |
| 4 | 150 | 0.56 | 0.82 | 27 | empty |
| 5 | 74 | 0.40 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 948 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 cofactor, 1 glycan (disulfide, retinal Schiff base, N-glycosylation).
Compared structures
- 6FUF · Crystal structure of the rhodopsin-mini-Go complex · the same entry in another collection · chain A against A, TM-score 1.00
- P09471 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(O) subunit… · a predicted model of the same protein · chain B against A, TM-score 0.88
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 P02699
- Every structure of UniProt P09471
- Elsewhere: RCSB PDB 6FUF · PDBe 6FUF · UniProt P02699 · UniProt P09471
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.