MolNFT v1 · #97722 · protein
Crystal structure of a blue-light absorbing proteorhodopsin double- mutant D97N/Q105L from HOT75
4KNF: “Crystal structure of a blue-light absorbing proteorhodopsin double- mutant D97N/Q105L from HOT75”. X-ray diffraction, 1 ligand (RET), 20 pockets (best druggability 0.82). MolNFT v1 #97722 on GenesisL1: 3D structure, binding sites…
- PDB
- 4KNF
- Type
- protein
- Length
- 1,146 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blue-light absorbing proteorhodopsin
- UniProt
- Q9AFF7
- Ligands
- RET
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Blue-light absorbing proteorhodopsin | protein | 231 | 81% helix, 0% strand | Q9AFF7 |
| B | Blue-light absorbing proteorhodopsin | protein | 224 | 80% helix, 0% strand | Q9AFF7 |
| C | Blue-light absorbing proteorhodopsin | protein | 232 | 83% helix, 0% strand | Q9AFF7 |
| D | Blue-light absorbing proteorhodopsin | protein | 229 | 81% helix, 0% strand | Q9AFF7 |
| E | Blue-light absorbing proteorhodopsin | protein | 230 | 83% helix, 0% strand | Q9AFF7 |
Ligands and binding sites
- RET · Retinal · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.82 | 0.98 | 24 | RET |
| 2 | 156 | 0.82 | 0.97 | 25 | RET |
| 3 | 139 | 0.81 | 0.97 | 22 | RET |
| 4 | 119 | 0.81 | 0.98 | 25 | RET |
| 5 | 128 | 0.80 | 0.97 | 24 | RET |
Interfaces
5 interfaces between chains.
- D–E · 898 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 889 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 885 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 867 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 863 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 cofactor (retinal Schiff base).
Compared structures
- 4KNF · Crystal structure of a blue-light absorbing proteorhodopsin double-mutant D97N/Q105L from… · the same entry in another collection · chain E against E, TM-score 1.00
- Q9AFF7 · AlphaFold monomer V2.0 prediction for blue-light absorbing proteorhodopsin (Q9AFF7) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 Q9AFF7
- Elsewhere: RCSB PDB 4KNF · PDBe 4KNF · UniProt Q9AFF7
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