Research workbench
Crystal structure of the light-driven inward proton pump xenorhodopsin BcXeR in the M state at pH 5.2 in the presence of sodium at 100K
Analyse Crystal structure of the light-driven inward proton pump xenorhodopsin BcXeR in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZNB
- Type
- protein
- Length
- 666 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Bacillus coahuilensis
- Molecule
- xenorhodopsin
- Ligands
- LFA, OLA, PO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.9 · 3 distinct chains · 79% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | xenorhodopsin | protein | 223 | 78% helix, 3% strand | — |
| B | xenorhodopsin | protein | 220 | 80% helix, 1% strand | — |
| C | xenorhodopsin | protein | 223 | 78% helix, 2% strand | — |
Ligands and binding sites
- LFA · Eicosane · ligand · 44 copies · chains A, C, B
- OLA · Oleic acid · ligand · 16 copies · chains A, C, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.71 | 0.76 | 55 | OLA, LFA |
| 2 | 748 | 0.70 | 0.76 | 54 | OLA, LFA |
| 3 | 732 | 0.70 | 0.76 | 56 | OLA, LFA |
| 4 | 146 | 0.52 | 0.79 | 20 | OLA, LFA |
| 5 | 172 | 0.51 | 0.77 | 23 | LFA, OLA |
Interfaces
3 interfaces between chains.
- A–B · 411 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 409 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 408 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (formylation, nonstandard).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7ZNB · PDBe 7ZNB
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