Research workbench
Crystal structure of exiguobacterium sibiricum rhodopsin
Analyse Crystal structure of exiguobacterium sibiricum rhodopsin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HYJ
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin
- UniProt
- B1YFV8
- Ligands
- LFA, RET
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin | protein | 236 | 84% helix, 0% strand | B1YFV8 |
| B | Rhodopsin | protein | 224 | 88% helix, 1% strand | B1YFV8 |
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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.84 | 0.85 | 96 | LFA |
| 2 | 120 | 0.80 | 0.97 | 26 | RET |
| 3 | 114 | 0.78 | 0.97 | 25 | RET |
| 4 | 122 | 0.42 | 0.76 | 23 | empty |
| 5 | 59 | 0.34 | 0.76 | 14 | LFA |
Interfaces
1 interface between chains.
- A–B · 945 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (retinal Schiff base).
Compared structures
- 4HYJ · Crystal structure of Exiguobacterium sibiricum rhodopsin · 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 B1YFV8
- Elsewhere: RCSB PDB 4HYJ · PDBe 4HYJ · UniProt B1YFV8
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