Research workbench
The crystal structure of cytochrome P450 105D7 from streptomyces avermitilis in complex with diclofenac
Analyse The crystal structure of cytochrome P450 105D7 from streptomyces avermitilis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UBS
- Type
- protein
- Length
- 393 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pentalenic acid synthase
- EC
- 1.14.15.11
- UniProt
- Q825I8
- Ligands
- DIF, HEM, PO4
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pentalenic acid synthase (EC 1.14.15.11) | protein | 393 | 53% helix, 10% strand | Q825I8 |
Ligands and binding sites
- DIF · 2-[2,6-dichlorophenyl)amino]benzeneacetic acid · ligand · 2 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 14 copies · chains A
- PGE · Triethylene glycol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.87 | 0.88 | 77 | HEM, DIF, PGE, PO4 |
| 2 | 66 | 0.48 | 0.84 | 20 | empty |
| 3 | 77 | 0.36 | 0.76 | 18 | empty |
| 4 | 83 | 0.35 | 0.76 | 21 | PEG |
| 5 | 52 | 0.34 | 0.78 | 14 | PEG |
Compared structures
- 4UBS · The crystal structure of cytochrome P450 105D7 from Streptomyces avermitilis in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q825I8 · AlphaFold monomer V2.0 prediction for pentalenic acid synthase (Q825I8) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q825I8
- Elsewhere: RCSB PDB 4UBS · PDBe 4UBS · UniProt Q825I8
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