Research workbench
Bacteriorhodopsin, 240FS state, real-space refined against 10% extrapolated MAP
Analyse Bacteriorhodopsin, 240FS state, real-space refined against 10% extrapolated MAP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GA7
- Type
- protein
- Length
- 231 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
- Molecule
- Bacteriorhodopsin
- UniProt
- P02945
- Ligands
- L2P, RET, TRD, D10, HP6, MYS, C14
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 74% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriorhodopsin | protein | 231 | 74% helix, 5% strand | P02945 |
Ligands and binding sites
- L2P · 2,3-di-phytanyl-glycerol · ligand · 3 copies · chains A
- RET · Retinal · ligand · chains A
- TRD · Tridecane · ligand · chains A
- D10 · Decane · ligand · chains A
- HP6 · Heptane · ligand · chains A
- MYS · Pentadecane · ligand · chains A
- C14 · Tetradecane · ligand · chains A
- OCT · N-octane · additive · 3 copies · chains A
- UND · Undecane · additive · 2 copies · chains A
- DD9 · nonane · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.81 | 0.98 | 22 | RET |
| 2 | 51 | 0.30 | 0.76 | 13 | empty |
Modifications
Observed in the structure: 1 cofactor (retinal Schiff base).
Compared structures
- 6GA7 · Bacteriorhodopsin, 240FS state, real-space refined against 10% extrapolated MAP · 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 1.00
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 6GA7 · PDBe 6GA7 · UniProt P02945
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