MolNFT v1 · #185692 · protein
Olep mutant G92W in complex with 6DEB
7Q89 · Cytochrome P-450: “Olep mutant G92W in complex with 6DEB”. X-ray diffraction, 3 ligands (HEM, DEB, NA), 20 pockets (best druggability 0.87). MolNFT v1 #185692 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7Q89
- Type
- protein
- Length
- 2,393 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P-450
- UniProt
- Q59819
- Ligands
- HEM, DEB, NA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Cytochrome P-450 | protein | 396 | 51% helix, 10% strand | Q59819 |
| B | Cytochrome P-450 | protein | 402 | 50% helix, 9% strand | Q59819 |
| C | Cytochrome P-450 | protein | 408 | 50% helix, 9% strand | Q59819 |
| E | Cytochrome P-450 | protein | 395 | 51% helix, 10% strand | Q59819 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
- DEB · 6-deoxyerythronolide B · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D, E, F
- FMT · Formic acid · additive · 139 copies · chains A, D, B, F, C, E
- GOL · Glycerol · additive · 9 copies · chains A, B, C, 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 | 779 | 0.87 | 0.90 | 68 | HEM, DEB, FMT, GOL |
| 2 | 699 | 0.87 | 0.90 | 64 | HEM, DEB |
| 3 | 789 | 0.87 | 0.89 | 73 | HEM, DEB, FMT, GOL |
| 4 | 702 | 0.87 | 0.90 | 54 | HEM, DEB |
| 5 | 714 | 0.86 | 0.89 | 57 | HEM, DEB, GOL |
Interfaces
5 interfaces between chains.
- D–E · 823 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 747 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 685 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 583 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 94 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7Q89 · OleP mutant G92W in complex with 6DEB · 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 Q59819
- Elsewhere: RCSB PDB 7Q89 · PDBe 7Q89 · UniProt Q59819
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