MolNFT v1 · #159137 · protein
Cryo-EM structure of the native rhodopsin dimer from rod photoreceptor cells
6OFJ: “Cryo-EM structure of the native rhodopsin dimer from rod photoreceptor cells”. Electron microscopy, 17 pockets (best druggability 0.87). MolNFT v1 #159137 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OFJ
- Type
- protein
- Length
- 650 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin
- UniProt
- P02699
- Pockets
- 17 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 64% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rhodopsin | protein | 325 | 64% helix, 2% strand | P02699 |
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.87 | 0.93 | 66 | empty |
| 2 | 578 | 0.87 | 0.92 | 69 | empty |
| 3 | 64 | 0.70 | 0.96 | 15 | empty |
| 4 | 70 | 0.70 | 0.95 | 15 | empty |
| 5 | 77 | 0.64 | 0.91 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 674 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6OFJ · Cryo-EM structure of the native rhodopsin dimer from rod photoreceptor cells · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 6OFJ · PDBe 6OFJ · UniProt P02699
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