Research workbench
The ground state and the N intermediate of pharaonis halorhodopsin in complex with bromide ion
Analyse The ground state and the N intermediate of pharaonis halorhodopsin in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QRY
- Type
- protein
- Length
- 1,557 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Halorhodopsin
- UniProt
- Q3ITX1
- Ligands
- RET, L2P, BNG, BR
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Halorhodopsin | protein | 261 | 28% helix, 69% strand | Q3ITX1 |
| B | Halorhodopsin | protein | 258 | 58% helix, 37% strand | Q3ITX1 |
| C, F, G | Halorhodopsin | protein | 259 | 40% helix, 51% strand | Q3ITX1 |
Ligands and binding sites
- RET · Retinal · ligand · 6 copies · chains A, E, B, F, C, G
- L2P · 2,3-di-phytanyl-glycerol · ligand · 6 copies · chains C, G, A, E, B, F
- BNG · nonyl beta-D-glucopyranoside · ligand · 5 copies · chains A, E, B, F, C, G
- BR · Bromide ion · ion · 12 copies · chains A, E, B, F, C, G
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 | 112 | 0.79 | 0.97 | 46 | RET |
| 2 | 105 | 0.79 | 0.98 | 44 | RET |
| 3 | 1047 | 0.78 | 0.79 | 196 | L2P |
| 4 | 96 | 0.77 | 0.97 | 41 | RET |
| 5 | 373 | 0.64 | 0.78 | 65 | BR |
Interfaces
15 interfaces between chains.
- C–G · 5747 Ų buried · 1,816 hydrogen bonds · protein-protein
- A–E · 5731 Ų buried · 1,868 hydrogen bonds · protein-protein
- B–F · 5683 Ų buried · 1,786 hydrogen bonds · protein-protein
- C–F · 829 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 823 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 cofactor, 9 disulfide (retinal Schiff base, disulfide).
Compared structures
- 4QRY · the ground state and the N intermediate of pharaonis halorhodopsin in complex with… · 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 4QRY · PDBe 4QRY · UniProt Q3ITX1
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