Research workbench
Crystal structure of oxyc a cytochrome P450 implicated in an oxidative C-C coupling reaction during vancomycin biosynthesis.
Analyse Crystal structure of oxyc a cytochrome P450 implicated in an oxidative C-C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UED
- Type
- protein
- Length
- 782 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P450 monooxygenase
- EC
- 1.14.-.-
- UniProt
- Q8RN03
- Ligands
- HEM
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P450 monooxygenase (EC 1.14.-.-) | protein | 391 | 54% helix, 10% strand | Q8RN03 |
| B | P450 monooxygenase (EC 1.14.-.-) | protein | 391 | 51% helix, 10% strand | Q8RN03 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.80 | 0.81 | 96 | HEM, PG4 |
| 2 | 1197 | 0.80 | 0.81 | 98 | HEM, PG4 |
| 3 | 558 | 0.68 | 0.78 | 45 | empty |
| 4 | 98 | 0.48 | 0.81 | 19 | empty |
| 5 | 67 | 0.41 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 309 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1UED · Crystal Structure of OxyC a Cytochrome P450 Implicated in an Oxidative C-C Coupling… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8RN03 · AlphaFold monomer V2.0 prediction for cytochrome P450 165C4 (Q8RN03) · 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 Q8RN03
- Elsewhere: RCSB PDB 1UED · PDBe 1UED · UniProt Q8RN03
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