GL1X · GenesisL1 explorer

Research workbench

P450 BM3 heme domain in complex with dmso

Analyse P450 BM3 heme domain in complex with dmso in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2J1M
Type
protein
Length
908 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Cytochrome P450 102
EC
1.14.14.1
UniProt
P14779
Ligands
HEM, ZN
Pockets
6 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 56% helix, 11% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BCytochrome P450 102 (EC 1.14.14.1)protein45456% helix, 11% strandP14779

Ligands and binding sites

  • HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
  • ZN · Zinc ion · metal · 7 copies · chains A, B
  • DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
110030.890.90105HEM, DMS
29290.870.8897HEM, DMS
32740.620.8027empty
42460.570.7826ZN
52410.510.7529empty

Interfaces

1 interface between chains.

  • A–B · 480 Ų buried · 10 hydrogen bonds · protein-protein

Compared structures

  • 2J1M · P450 BM3 Heme domain in complex with DMSO · the same entry in another collection · chain A against A, TM-score 1.00
  • P14779 · AlphaFold monomer V2.0 prediction for bifunctional cytochrome P450/NADPH--P450 reductase… · a predicted model of the same protein · chain B against A, TM-score 0.99

Analyse

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