MolNFT v1 · #116853 · protein

Polyethylene 600-bound form of P450 CYP125A3 mutant from myobacterium smegmatis - W83Y

5DQN · Cytochrome P450 CYP125: “Polyethylene 600-bound form of P450 CYP125A3 mutant from myobacterium smegmatis - W83Y”. X-ray diffraction, 2 ligands (HEM, PO4), 3 pockets (best druggability 0.83). MolNFT v1 #116853 on GenesisL1: 3D…

PDB: 5DQN
Type: protein
Length: 410 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome P450 CYP125
EC: 1.14.13.151
UniProt: I7G9K1
Ligands: HEM, PO4
Pockets: 3 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome P450 CYP125 (EC 1.14.13.151)	protein	410	49% helix, 11% strand	I7G9K1

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A
PO4 · Phosphate ion · ion · 2 copies · chains A
CIT · Citric acid · additive · chains A
1PE · Pentaethylene glycol · additive · 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	832	0.83	0.85	91	HEM, PO4, 1PE
2	88	0.47	0.81	19	empty
3	159	0.45	0.75	21	empty

Compared structures

5DQN · Polyethylene 600-bound form of P450 CYP125A3 mutant from Myobacterium Smegmatis - W83Y · 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 I7G9K1
Elsewhere: RCSB PDB 5DQN · PDBe 5DQN · UniProt I7G9K1

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