MolNFT v1 · #107488 · protein
The crystal structure of cytochrome P450 105D7 from streptomyces avermitilis in complex with diclofenac
4UBS · Pentalenic acid synthase: “The crystal structure of cytochrome P450 105D7 from streptomyces avermitilis in complex with diclofenac”. X-ray diffraction, 3 ligands (DIF, HEM, PO4), 5 pockets (best druggability 0.87). MolNFT v1 #107488…
- 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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