Research workbench
Crystal structure of H. walsbyi bacteriorhodopsin
Analyse Crystal structure of H. walsbyi bacteriorhodopsin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QI1
- Type
- protein
- Length
- 684 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriorhodopsin-I
- UniProt
- Q18DH8
- Ligands
- MPG, RET
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Bacteriorhodopsin-I | protein | 228 | 77% helix, 4% strand | Q18DH8 |
Ligands and binding sites
- MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 9 copies · chains A, C, B
- RET · Retinal · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.81 | 0.98 | 24 | RET |
| 2 | 141 | 0.81 | 0.98 | 26 | RET |
| 3 | 138 | 0.80 | 0.97 | 23 | RET |
| 4 | 624 | 0.78 | 0.83 | 65 | MPG |
| 5 | 413 | 0.73 | 0.83 | 44 | MPG |
Interfaces
3 interfaces between chains.
- A–B · 581 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 566 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 560 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 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 4QI1 · PDBe 4QI1 · UniProt Q18DH8
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