MolNFT v1 · #173444 · protein
Cryo-EM structure of the green-light absorbing proteorhodopsin
7B03: “Cryo-EM structure of the green-light absorbing proteorhodopsin”. Electron microscopy, 1 ligand (RET), 20 pockets (best druggability 0.80). MolNFT v1 #173444 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7B03
- Type
- protein
- Length
- 1,085 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteorhodopsin
- UniProt
- Q6J4G7
- Ligands
- RET
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Proteorhodopsin | protein | 217 | 83% helix, 0% strand | Q6J4G7 |
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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.80 | 0.96 | 23 | RET |
| 2 | 154 | 0.79 | 0.95 | 24 | RET |
| 3 | 211 | 0.79 | 0.93 | 34 | RET |
| 4 | 217 | 0.79 | 0.92 | 33 | RET |
| 5 | 203 | 0.78 | 0.92 | 31 | RET |
Interfaces
5 interfaces between chains.
- D–E · 842 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 842 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 842 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 835 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 830 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 cofactor (retinal Schiff base).
Compared structures
- 7B03 · Cryo-EM structure of the green-light absorbing proteorhodopsin · 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 Q6J4G7
- Elsewhere: RCSB PDB 7B03 · PDBe 7B03 · UniProt Q6J4G7
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