MolNFT v1 · #96660 · protein
Crystal structure of blue light-absorbing proteorhodopsin from MED12 at 2.3 ångström
4JQ6: “Crystal structure of blue light-absorbing proteorhodopsin from MED12 at 2.3 ångström”. X-ray diffraction, 2 ligands (RET, LI1), 9 pockets (best druggability 0.81). MolNFT v1 #96660 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4JQ6
- Type
- protein
- Length
- 599 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteorhodopsin
- UniProt
- Q4PP54
- Ligands
- RET, LI1
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 87% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteorhodopsin | protein | 197 | 85% helix, 0% strand | Q4PP54 |
| B | Proteorhodopsin | protein | 203 | 87% helix, 0% strand | Q4PP54 |
| C | Proteorhodopsin | protein | 199 | 87% helix, 0% strand | Q4PP54 |
Ligands and binding sites
- RET · Retinal · ligand · 3 copies · chains A, B, C
- LI1 · 1-[2,6,10.14-tetramethyl-hexadecan-16-yl]-2-[2,10,14-trimethylhexadecan-16-yl]glycerol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.81 | 0.99 | 22 | RET |
| 2 | 139 | 0.81 | 0.98 | 22 | RET |
| 3 | 134 | 0.81 | 0.98 | 23 | RET |
| 4 | 870 | 0.78 | 0.80 | 64 | empty |
| 5 | 887 | 0.77 | 0.79 | 68 | empty |
Interfaces
2 interfaces between chains.
- A–B · 787 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 766 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (retinal Schiff base).
Compared structures
- 4JQ6 · Crystal structure of blue light-absorbing proteorhodopsin from Med12 at 2.3 Angstrom · 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 Q4PP54
- Elsewhere: RCSB PDB 4JQ6 · PDBe 4JQ6 · UniProt Q4PP54
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