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Anion free form of light-driven chloride ion-pumping rhodopsin, nm-R3, structure determined by serial femtosecond crystallography at sacla
Analyse Anion free form of light-driven chloride ion-pumping rhodopsin, nm-R3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VGV
- Type
- protein
- Length
- 791 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chloride pumping rhodopsin
- UniProt
- W8VZW3
- Ligands
- RET, C14, R16, CL
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 82% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Chloride pumping rhodopsin | protein | 264 | 82% helix, 3% strand | W8VZW3 |
| B | Chloride pumping rhodopsin | protein | 263 | 81% helix, 4% strand | W8VZW3 |
Ligands and binding sites
- RET · Retinal · ligand · 3 copies · chains A, B, C
- C14 · Tetradecane · ligand · 2 copies · chains A, B
- R16 · Hexadecane · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains C
- HEX · Hexane · additive · 6 copies · chains A, C, B
- DD9 · nonane · additive · 3 copies · chains A, B
- OCT · N-octane · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.74 | 0.79 | 76 | DD9, RET, OCT |
| 2 | 125 | 0.73 | 0.93 | 22 | RET |
| 3 | 125 | 0.73 | 0.92 | 25 | RET |
| 4 | 259 | 0.55 | 0.76 | 26 | HEX, DD9 |
| 5 | 53 | 0.37 | 0.80 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 612 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 359 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (retinal Schiff base).
Compared structures
- 7VGV · Anion free form of light-driven chloride ion-pumping rhodopsin, NM-R3, structure… · 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 W8VZW3
- Elsewhere: RCSB PDB 7VGV · PDBe 7VGV · UniProt W8VZW3
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