MolNFT v1 · #76134 · protein
Crystal structure of an anion-free yellow form of pharaonis halorhodopsin
3QBI: “Crystal structure of an anion-free yellow form of pharaonis halorhodopsin”. X-ray diffraction, 3 ligands (BNG, RET, 22B), 10 pockets (best druggability 0.79). MolNFT v1 #76134 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3QBI
- Type
- protein
- Length
- 781 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Halorhodopsin
- UniProt
- Q3ITX1
- Ligands
- BNG, RET, 22B
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Halorhodopsin | protein | 261 | 73% helix, 5% strand | Q3ITX1 |
| B, D | Halorhodopsin | protein | 260 | 73% helix, 4% strand | Q3ITX1 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 4 copies · chains A, D, B
- RET · Retinal · ligand · 3 copies · chains A, B, D
- 22B · Bacterioruberin · ligand · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.79 | 0.97 | 22 | RET |
| 2 | 125 | 0.79 | 0.97 | 21 | RET |
| 3 | 138 | 0.79 | 0.96 | 23 | RET |
| 4 | 389 | 0.64 | 0.78 | 31 | 22B |
| 5 | 266 | 0.63 | 0.80 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–D · 825 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 787 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 756 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (retinal Schiff base).
Compared structures
- 3QBI · Crystal structure of an anion-free yellow 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 3QBI · PDBe 3QBI · UniProt Q3ITX1
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