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X-ray structure of the substrate-bound cytochrome P450 pimd - a polyene macrolide antibiotic pimaricin epoxidase

Analyse X-ray structure of the substrate-bound cytochrome P450 pimd - a polyene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XBK
Type: protein
Length: 391 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pimd protein
UniProt: Q9EW92
Ligands: HEM, XBK
Pockets: 4 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pimd protein	protein	391	53% helix, 12% strand	Q9EW92

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A
XBK · 4,5-de-epoxypimaricin · ligand · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1155	0.85	0.86	96	HEM, XBK
2	70	0.52	0.85	19	empty
3	65	0.41	0.80	14	empty
4	60	0.35	0.78	13	empty

Compared structures

2XBK · X-ray structure of the substrate-bound cytochrome P450 PimD - a polyene macrolide… · 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 Q9EW92
Elsewhere: RCSB PDB 2XBK · PDBe 2XBK · UniProt Q9EW92

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