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Crystal structure of oxyb, a cytochrome P450 implicated in an oxidative phenol coupling reaction during vancomycin biosynthesis

Analyse Crystal structure of oxyb, a cytochrome P450 implicated in an oxidative phenol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1LGF
Type: protein
Length: 388 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: P450 monooxygenase
UniProt: Q8RN04
Ligands: HEM
Pockets: 3 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	P450 monooxygenase	protein	388	50% helix, 11% strand	Q8RN04

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1097	0.84	0.85	111	HEM
2	88	0.39	0.77	20	empty
3	51	0.27	0.74	11	empty

Compared structures

1LGF · Crystal structure of OxyB, a Cytochrome P450 Implicated in an Oxidative Phenol Coupling… · the same entry in another collection · chain A against A, TM-score 1.00
Q8RN04 · AlphaFold monomer V2.0 prediction for cytochrome P450 165B3 (Q8RN04) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 Q8RN04
Elsewhere: RCSB PDB 1LGF · PDBe 1LGF · UniProt Q8RN04

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