MolNFT v1 · #177000 · protein
Crystal structure of schizorhodopsin 4
7E4G: “Crystal structure of schizorhodopsin 4”. X-ray diffraction, 3 ligands (RET, ZN, SO4), 8 pockets (best druggability 0.77). MolNFT v1 #177000 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7E4G
- Type
- protein
- Length
- 588 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Schizorhodopsin 4
- Ligands
- RET, ZN, SO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 77% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Schizorhodopsin 4 | protein | 199 | 78% helix, 2% strand | — |
| B | Schizorhodopsin 4 | protein | 196 | 77% helix, 2% strand | — |
| C | Schizorhodopsin 4 | protein | 193 | 77% helix, 2% strand | — |
Ligands and binding sites
- RET · Retinal · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, C
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 32 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.77 | 0.94 | 23 | RET |
| 2 | 139 | 0.76 | 0.94 | 27 | RET |
| 3 | 130 | 0.76 | 0.94 | 24 | RET |
| 4 | 836 | 0.71 | 0.75 | 66 | OLC |
| 5 | 125 | 0.43 | 0.75 | 22 | OLC |
Interfaces
3 interfaces between chains.
- A–C · 910 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 897 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 878 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (retinal Schiff base).
Compared structures
- 7E4G · Crystal structure of schizorhodopsin 4 · 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
- Elsewhere: RCSB PDB 7E4G · PDBe 7E4G
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