Research workbench
Crystal structure of haloquadratum walsbyi bacteriorhodopsin
Analyse Crystal structure of haloquadratum walsbyi bacteriorhodopsin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QID
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriorhodopsin-I
- UniProt
- Q18DH8
- Ligands
- RET, MPG
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriorhodopsin-I | protein | 228 | 76% helix, 4% strand | Q18DH8 |
| B | Bacteriorhodopsin-I | protein | 224 | 76% helix, 3% strand | Q18DH8 |
Ligands and binding sites
- RET · Retinal · ligand · 2 copies · chains A, B
- MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · chains B
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.82 | 0.98 | 25 | RET |
| 2 | 119 | 0.80 | 0.97 | 24 | RET |
| 3 | 152 | 0.51 | 0.78 | 24 | empty |
| 4 | 78 | 0.40 | 0.79 | 24 | empty |
| 5 | 79 | 0.40 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 766 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (retinal Schiff base).
Compared structures
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 Q18DH8
- Elsewhere: RCSB PDB 4QID · PDBe 4QID · UniProt Q18DH8
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