Research workbench
X-ray structure of the bacteriorhodopsin TRIMER/LIPID complex
Analyse X-ray structure of the bacteriorhodopsin TRIMER/LIPID complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BRR
- Type
- protein
- Length
- 693 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (bacteriorhodopsin)
- UniProt
- P02945
- Ligands
- ARC, RET, SGA, GLC, MAN, BGC
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (bacteriorhodopsin) | protein | 230 | 72% helix, 3% strand | P02945 |
| B | Protein (bacteriorhodopsin) | protein | 231 | 73% helix, 5% strand | P02945 |
| C | Protein (bacteriorhodopsin) | protein | 232 | 70% helix, 5% strand | P02945 |
Ligands and binding sites
- ARC · 3,7,11,15-tetramethyl-hexadecan-1-ol · ligand · 10 copies · chains A, C, B
- RET · Retinal · ligand · 3 copies · chains A, B, C
- SGA · 3-O-sulfo-beta-D-galactopyranose · ligand · 2 copies · chains B, A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B, C
- BGC · beta-D-glucopyranose · sugar · chains B
- GOL · Glycerol · additive · 3 copies · chains A, B, C
- OCT · N-octane · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.81 | 0.98 | 23 | RET |
| 2 | 125 | 0.81 | 0.98 | 26 | RET |
| 3 | 115 | 0.81 | 0.99 | 21 | RET |
| 4 | 1099 | 0.76 | 0.78 | 84 | ARC, GOL |
| 5 | 433 | 0.69 | 0.80 | 40 | ARC |
Interfaces
3 interfaces between chains.
- A–B · 737 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 737 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 737 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 cofactor, 1 modified (retinal Schiff base, cyclization).
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 P02945
- Elsewhere: RCSB PDB 1BRR · PDBe 1BRR · UniProt P02945
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