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Human cytochrome P450 2A13 in complex with pilocarpine

Analyse Human cytochrome P450 2A13 in complex with pilocarpine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3T3S
Type: protein
Length: 3,712 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome P450 2A13
EC: 1.14.14.1
UniProt: Q16696
Ligands: HEM, 9PL
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Cytochrome P450 2A13 (EC 1.14.14.1)	protein	464	49% helix, 10% strand	Q16696

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
9PL · (3S,4R)-3-ethyl-4-[(1-methyl-1H-imidazol-5-yl)methyl]dihydrofuran-2(3H)-one · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	460	0.87	0.93	49	HEM, 9PL
2	432	0.86	0.93	49	HEM, 9PL
3	431	0.86	0.93	51	HEM, 9PL
4	417	0.86	0.93	49	HEM, 9PL
5	425	0.85	0.93	54	HEM, 9PL

Interfaces

10 interfaces between chains.

A–B · 879 Å² buried · 10 hydrogen bonds · protein-protein
E–H · 821 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 752 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 738 Å² buried · 11 hydrogen bonds · protein-protein
D–G · 452 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3T3S · Human Cytochrome P450 2A13 in complex with Pilocarpine · the same entry in another collection · chain H against H, TM-score 1.00
Q16696 · AlphaFold monomer V2.0 prediction for cytochrome P450 2A13 (Q16696) · a predicted model of the same protein · 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 Q16696
Elsewhere: RCSB PDB 3T3S · PDBe 3T3S · UniProt Q16696

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