Research workbench
Crystal structure of haloquadratum walsbyi bacteriorhodopsin mutant D93N
Analyse Crystal structure of haloquadratum walsbyi bacteriorhodopsin mutant D93N in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WAV
- Type
- protein
- Length
- 453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriorhodopsin-I
- UniProt
- G0LFX8
- Ligands
- RET, MPG
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriorhodopsin-I | protein | 227 | 74% helix, 3% strand | G0LFX8 |
| B | Bacteriorhodopsin-I | protein | 226 | 73% helix, 4% strand | G0LFX8 |
Ligands and binding sites
- RET · Retinal · ligand · 2 copies · chains A, B
- MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.81 | 0.98 | 25 | RET |
| 2 | 125 | 0.80 | 0.98 | 25 | RET |
| 3 | 176 | 0.53 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 846 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (retinal Schiff base).
Compared structures
- 4WAV · Crystal Structure of Haloquadratum walsbyi bacteriorhodopsin mutant D93N · the same entry in another collection · chain A against A, TM-score 1.00
- G0LFX8 · AlphaFold monomer V2.0 prediction for bacteriorhodopsin-I (G0LFX8) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 G0LFX8
- Elsewhere: RCSB PDB 4WAV · PDBe 4WAV · UniProt G0LFX8
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