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

Analyse X-ray structure of the substrate-free 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: 2X9P
Type: protein
Length: 385 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pimd protein
UniProt: Q9EW92
Ligands: HEM, SO4
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 56% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pimd protein	protein	385	56% helix, 10% strand	Q9EW92

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A
SO4 · Sulfate ion · ion · 3 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	818	0.80	0.83	71	HEM
2	127	0.61	0.85	18	empty
3	59	0.45	0.83	21	empty
4	71	0.39	0.78	12	empty
5	63	0.35	0.77	19	empty

Compared structures

2X9P · X-ray structure of the substrate-free 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 2X9P · PDBe 2X9P · UniProt Q9EW92

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