MolNFT v1 · #82722 · protein
An M-like reaction state of the azide-bound purple form of pharaonis halorhodopsin
3VVK: “An M-like reaction state of the azide-bound purple form of pharaonis halorhodopsin”. X-ray diffraction, 5 ligands (RET, BNG, L3P), 8 pockets (best druggability 0.80). MolNFT v1 #82722 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3VVK
- Type
- protein
- Length
- 1,556 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Halorhodopsin
- UniProt
- Q3ITX1
- Ligands
- RET, BNG, L3P, 22B, AZI
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Halorhodopsin | protein | 261 | 43% helix, 54% strand | Q3ITX1 |
| B | Halorhodopsin | protein | 258 | 53% helix, 40% strand | Q3ITX1 |
| C, E, F | Halorhodopsin | protein | 259 | 32% helix, 63% strand | Q3ITX1 |
| D | Halorhodopsin | protein | 260 | 57% helix, 39% strand | Q3ITX1 |
Ligands and binding sites
- RET · Retinal · ligand · 6 copies · chains A, D, B, E, C, F
- BNG · nonyl beta-D-glucopyranoside · ligand · 4 copies · chains A, D, C, F, B, E
- L3P · 2,3-di-O-phytanly-3-sn-glycero-1-phosphoryl-3'-sn-glycerol-1'-phosphate · ligand · 4 copies · chains B, C, E, F, A, D
- 22B · Bacterioruberin · ligand · 2 copies · chains A, C, D, F, B, E
- AZI · Azide ion · ion · 3 copies · chains A, D, B, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.80 | 0.98 | 40 | RET |
| 2 | 97 | 0.78 | 0.98 | 39 | RET |
| 3 | 1063 | 0.77 | 0.79 | 179 | L3P |
| 4 | 86 | 0.77 | 0.98 | 37 | RET |
| 5 | 391 | 0.67 | 0.79 | 60 | 22B |
Interfaces
15 interfaces between chains.
- A–D · 5749 Ų buried · 1,852 hydrogen bonds · protein-protein
- C–F · 5702 Ų buried · 1,819 hydrogen bonds · protein-protein
- B–E · 5683 Ų buried · 1,821 hydrogen bonds · protein-protein
- E–F · 851 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 817 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 cofactor, 9 disulfide (retinal Schiff base, disulfide).
Compared structures
- 3VVK · An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin · 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 Q3ITX1
- Elsewhere: RCSB PDB 3VVK · PDBe 3VVK · UniProt Q3ITX1
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