Research workbench
Crystal structure of the inward H(+) pump xenorhodopsin
Analyse Crystal structure of the inward H(+) pump xenorhodopsin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EYU
- Type
- protein
- Length
- 693 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriorhodopsin
- UniProt
- G0QG75
- Ligands
- MUN, LFA, RET
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bacteriorhodopsin | protein | 232 | 80% helix, 1% strand | G0QG75 |
| C | Bacteriorhodopsin | protein | 229 | 81% helix, 1% strand | G0QG75 |
Ligands and binding sites
- MUN · [(2~{S})-2,3-bis(oxidanyl)propyl] (~{E})-undec-2-enoate · ligand · 26 copies · chains A, B, C
- LFA · Eicosane · ligand · 12 copies · chains A, B, C
- RET · Retinal · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.80 | 0.97 | 21 | RET |
| 2 | 130 | 0.80 | 0.97 | 19 | RET |
| 3 | 114 | 0.80 | 0.98 | 21 | RET |
| 4 | 1182 | 0.77 | 0.78 | 85 | LFA, MUN |
| 5 | 195 | 0.54 | 0.78 | 23 | MUN |
Interfaces
3 interfaces between chains.
- A–B · 681 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 674 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 673 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (retinal Schiff base).
Compared structures
- 6EYU · Crystal structure of the inward H(+) pump xenorhodopsin · the same entry in another collection · 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 G0QG75
- Elsewhere: RCSB PDB 6EYU · PDBe 6EYU · UniProt G0QG75
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