Research workbench

Recombinant horseradish peroxidase complex with benzhydroxamic acid

Analyse Recombinant horseradish peroxidase complex with benzhydroxamic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ATJ
Type: protein
Length: 616 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxidase C1A
EC: 1.11.1.7
UniProt: P00433
Ligands: HEM, BHO, CA
Pockets: 4 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Peroxidase C1A (EC 1.11.1.7)	protein	308	49% helix, 4% strand	P00433

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
BHO · Benzhydroxamic acid · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 4 copies · chains A, B

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

Pockets

4 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	932	0.84	0.85	79	HEM, BHO
2	355	0.82	0.91	42	HEM, BHO
3	386	0.59	0.76	44	empty
4	52	0.41	0.82	15	empty

Interfaces

1 interface between chains.

A–B · 471 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

2ATJ · Recombinant horseradish peroxidase complex with benzhydroxamic acid · the same entry in another collection · chain A against A, TM-score 1.00
P00433 · AlphaFold monomer V2.0 prediction for peroxidase C1A (P00433) · 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 P00433
Elsewhere: RCSB PDB 2ATJ · PDBe 2ATJ · UniProt P00433

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