MolNFT v1 · #147606 · protein
Crystal structure of wild-type channelrhodopsin 2
6EID · Archaeal-type opsin 2: “Crystal structure of wild-type channelrhodopsin 2”. X-ray diffraction, 2 ligands (EDT, PO4), 6 pockets (best druggability 0.82). MolNFT v1 #147606 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6EID
- Type
- protein
- Length
- 498 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Archaeal-type opsin 2
- UniProt
- Q8RUT8
- Ligands
- EDT, PO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Archaeal-type opsin 2 | protein | 247 | 76% helix, 2% strand | Q8RUT8 |
| B | Archaeal-type opsin 2 | protein | 251 | 75% helix, 2% strand | Q8RUT8 |
Ligands and binding sites
- EDT · {[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid · ligand · chains A
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.82 | 0.82 | 73 | OLC |
| 2 | 91 | 0.46 | 0.81 | 16 | empty |
| 3 | 82 | 0.42 | 0.79 | 15 | empty |
| 4 | 55 | 0.35 | 0.79 | 15 | empty |
| 5 | 73 | 0.31 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 607 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6EID · Crystal structure of wild-type Channelrhodopsin 2 · 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 Q8RUT8
- Elsewhere: RCSB PDB 6EID · PDBe 6EID · UniProt Q8RUT8
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