MolNFT v1 · #111514 · protein

CYP106A2

4YT3 · Cytochrome P450(MEG): “CYP106A2”. X-ray diffraction, 1 ligand (HEM), 7 pockets (best druggability 0.79). MolNFT v1 #111514 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4YT3
Type: protein
Length: 776 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome P450(MEG)
EC: 1.14.99.-, 1.14.15.8
UniProt: Q06069
Ligands: HEM
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 55% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome P450(MEG) (EC 1.14.99.-, 1.14.15.8)	protein	388	55% helix, 11% strand	Q06069
B	Cytochrome P450(MEG) (EC 1.14.99.-, 1.14.15.8)	protein	388	55% helix, 11% strand	Q06069

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
ACT · Acetate ion · additive · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	780	0.79	0.82	72	HEM
2	716	0.76	0.81	67	HEM
3	489	0.61	0.75	61	ACT
4	63	0.45	0.83	14	empty
5	81	0.35	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 883 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4YT3 · CYP106A2 · the same entry in another collection · chain A against A, TM-score 1.00
Q06069 · AlphaFold monomer V2.0 prediction for cytochrome P450(MEG) (Q06069) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q06069
Elsewhere: RCSB PDB 4YT3 · PDBe 4YT3 · UniProt Q06069

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