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Crystallographic structure of xanthorhodopsin, a light-driven ion pump with dual chromophore
Analyse Crystallographic structure of xanthorhodopsin, a light-driven ion pump with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DDL
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xanthorhodopsin
- UniProt
- Q2S2F8
- Ligands
- UNL, SXN, RET, PX4, PCW
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xanthorhodopsin | protein | 252 | 78% helix, 3% strand | Q2S2F8 |
| B | Xanthorhodopsin | protein | 250 | 79% helix, 3% strand | Q2S2F8 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 21 copies · chains A, B
- SXN · Salinixanthin · ligand · 2 copies · chains A, B
- RET · Retinal · ligand · 2 copies · chains A, B
- PX4 · 1,2-dimyristoyl-sn-glycero-3-phosphocholine · ligand · chains B
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.75 | 0.92 | 27 | RET |
| 2 | 169 | 0.74 | 0.90 | 29 | RET |
| 3 | 854 | 0.72 | 0.77 | 75 | UNL |
| 4 | 326 | 0.62 | 0.78 | 29 | empty |
| 5 | 107 | 0.39 | 0.75 | 18 | UNL |
Interfaces
1 interface between chains.
- A–B · 657 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (retinal Schiff base).
Compared structures
- 3DDL · Crystallographic Structure of Xanthorhodopsin, a Light-Driven Ion Pump with Dual… · 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 Q2S2F8
- Elsewhere: RCSB PDB 3DDL · PDBe 3DDL · UniProt Q2S2F8
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