MolNFT v1 · #18301 · protein

Crystal structure of epothilone D-bound cytochrome P450EPOK

1PKF: “Crystal structure of epothilone D-bound cytochrome P450EPOK”. X-ray diffraction, 2 ligands (HEM, EPD), 6 pockets (best druggability 0.86). MolNFT v1 #18301 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PKF
Type: protein
Length: 403 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome P450EPOK
UniProt: Q9KIZ4
Ligands: HEM, EPD
Pockets: 6 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 55% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome P450EPOK	protein	403	55% helix, 10% strand	Q9KIZ4

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A
EPD · Epothilone D · ligand · chains A

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

Pockets

6 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	739	0.86	0.90	63	HEM, EPD
2	125	0.50	0.81	21	empty
3	130	0.40	0.74	17	empty
4	57	0.33	0.77	15	empty
5	72	0.32	0.75	13	empty

Compared structures

1PKF · Crystal Structure of Epothilone D-bound Cytochrome P450epoK · the same entry in another collection · chain A against A, TM-score 1.00
Q9KIZ4 · AlphaFold monomer V2.0 prediction for epothilone C/D epoxidase (Q9KIZ4) · 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 Q9KIZ4
Elsewhere: RCSB PDB 1PKF · PDBe 1PKF · UniProt Q9KIZ4

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