MolNFT v1 · #84596 · protein

Pikc D50N mutant in P21 space group

3ZPI · Cytochrome P450 hydroxylase pikc: “Pikc D50N mutant in P21 space group”. X-ray diffraction, 2 ligands (HEM, NA), 5 pockets (best druggability 0.87). MolNFT v1 #84596 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3ZPI
Type: protein
Length: 792 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome P450 hydroxylase pikc
UniProt: O87605
Ligands: HEM, NA
Pockets: 5 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 54% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome P450 hydroxylase pikc	protein	396	54% helix, 10% strand	O87605
B	Cytochrome P450 hydroxylase pikc	protein	396	54% helix, 10% strand	O87605

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · chains A
FMT · Formic acid · additive · 8 copies · chains A, B
EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
TLA · L(+)-tartaric acid · additive · 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	940	0.87	0.88	81	HEM
2	826	0.86	0.89	71	HEM
3	429	0.77	0.86	40	FMT
4	246	0.67	0.84	28	empty
5	53	0.56	0.90	13	empty

Interfaces

1 interface between chains.

A–B · 359 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3ZPI · PikC D50N mutant in P21 space group · the same entry in another collection · chain A against A, TM-score 1.00
O87605 · AlphaFold monomer V2.0 prediction for cytochrome P450 monooxygenase pikc (O87605) · a predicted model of the same protein · chain B 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 O87605
Elsewhere: RCSB PDB 3ZPI · PDBe 3ZPI · UniProt O87605

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.