MolNFT v1 · #48014 · protein

Crystal structure of human microsomal P450 2A6 N297Q

2PG5 · Cytochrome P450 2A6: “Crystal structure of human microsomal P450 2A6 N297Q”. X-ray diffraction, 1 ligand (HEM), 17 pockets (best druggability 0.86). MolNFT v1 #48014 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2PG5
Type: protein
Length: 1,855 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome P450 2A6
EC: 1.14.14.1
UniProt: P11509
Ligands: HEM
Pockets: 17 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Cytochrome P450 2A6 (EC 1.14.14.1)	protein	464	53% helix, 10% strand	P11509
B	Cytochrome P450 2A6 (EC 1.14.14.1)	protein	464	53% helix, 10% strand	P11509
C	Cytochrome P450 2A6 (EC 1.14.14.1)	protein	463	53% helix, 11% strand	P11509

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D

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

Pockets

17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	418	0.86	0.94	46	HEM, EDO
2	419	0.86	0.93	42	HEM, EDO
3	425	0.86	0.93	48	HEM, EDO
4	427	0.85	0.92	51	HEM, EDO
5	1142	0.77	0.78	54	empty

Interfaces

5 interfaces between chains.

A–B · 646 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 416 Å² buried · 1 hydrogen bond · protein-protein
B–C · 399 Å² buried · 1 hydrogen bond · protein-protein
B–D · 189 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 176 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2PG5 · Crystal Structure of Human Microsomal P450 2A6 N297Q · the same entry in another collection · chain C against C, TM-score 1.00
P11509 · AlphaFold monomer V2.0 prediction for cytochrome P450 2A6 (P11509) · a predicted model of the same protein · chain C 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 P11509
Elsewhere: RCSB PDB 2PG5 · PDBe 2PG5 · UniProt P11509

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