Research workbench
Crystal structure analysis of the bacteriorhodopsin in facial amphiphile-4 dmpc bicelle
Analyse Crystal structure analysis of the bacteriorhodopsin in facial amphiphile-4 dmpc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HYX
- Type
- protein
- Length
- 457 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriorhodopsin
- UniProt
- P02945
- Ligands
- D10, RET, C14
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriorhodopsin | protein | 226 | 77% helix, 5% strand | P02945 |
| B | Bacteriorhodopsin | protein | 231 | 76% helix, 5% strand | P02945 |
Ligands and binding sites
- D10 · Decane · ligand · 8 copies · chains A, B
- RET · Retinal · ligand · 2 copies · chains A, B
- C14 · Tetradecane · ligand · chains B
- OCT · N-octane · additive · 4 copies · chains A, B
- HEX · Hexane · additive · chains B
- GOL · Glycerol · additive · chains B
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 | 130 | 0.81 | 0.98 | 22 | RET |
| 2 | 117 | 0.80 | 0.98 | 20 | RET |
| 3 | 623 | 0.68 | 0.76 | 69 | D10 |
Interfaces
1 interface between chains.
- A–B · 715 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (retinal Schiff base).
Compared structures
- 4HYX · Crystal Structure Analysis of the Bacteriorhodopsin in Facial Amphiphile-4 DMPC Bicelle · the same entry in another collection · chain A against A, TM-score 1.00
- P02945 · AlphaFold monomer V2.0 prediction for bacteriorhodopsin (P02945) · a predicted model of the same protein · chain A 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 P02945
- Elsewhere: RCSB PDB 4HYX · PDBe 4HYX · UniProt P02945
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