Research workbench
Crystal structure of the viral rhodopsin OLPVR1 in P1 space group
Analyse Crystal structure of the viral rhodopsin OLPVR1 in P1 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AKX
- Type
- protein
- Length
- 448 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Viral rhodopsin OLPVR1
- UniProt
- F2Y337
- Ligands
- LFA, OLA
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Viral rhodopsin OLPVR1 | protein | 224 | 84% helix, 0% strand | F2Y337 |
Ligands and binding sites
- LFA · Eicosane · ligand · 26 copies · chains A, B
- OLA · Oleic acid · ligand · 4 copies · chains A, B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.81 | 0.82 | 74 | LFA, OLA |
| 2 | 85 | 0.57 | 0.86 | 16 | OLA |
Interfaces
1 interface between chains.
- A–B · 485 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 7AKX · Crystal structure of the viral rhodopsin OLPVR1 in P1 space group · 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 F2Y337
- Elsewhere: RCSB PDB 7AKX · PDBe 7AKX · UniProt F2Y337
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