Research workbench
Olep mutant S240Y in complex with 6DEB
Analyse Olep mutant S240Y in complex with 6DEB in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q6X
- Type
- protein
- Length
- 2,390 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P-450
- UniProt
- Q59819
- Ligands
- HEM, DEB
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Cytochrome P-450 | protein | 397 | 49% helix, 10% strand | Q59819 |
| B | Cytochrome P-450 | protein | 406 | 49% helix, 9% strand | Q59819 |
| C | Cytochrome P-450 | protein | 399 | 50% helix, 10% strand | Q59819 |
| D | Cytochrome P-450 | protein | 396 | 48% helix, 10% strand | Q59819 |
| E | Cytochrome P-450 | protein | 395 | 47% 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
- FMT · Formic acid · additive · 6 copies · chains A, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.87 | 0.90 | 65 | HEM, DEB |
| 2 | 760 | 0.87 | 0.90 | 65 | HEM, DEB |
| 3 | 738 | 0.87 | 0.90 | 64 | HEM, DEB |
| 4 | 726 | 0.87 | 0.90 | 64 | HEM, DEB |
| 5 | 705 | 0.87 | 0.90 | 62 | HEM, DEB |
Interfaces
5 interfaces between chains.
- B–C · 887 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 844 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 776 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 572 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 89 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (heme attachment).
Compared structures
- 7Q6X · OleP mutant S240Y 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 7Q6X · PDBe 7Q6X · UniProt Q59819
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.