Research workbench

Recombinant horseradish peroxidase C1A

Analyse Recombinant horseradish peroxidase C1A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ATJ
Type: protein
Length: 1,836 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxidase C1A
EC: 1.11.1.7
UniProt: P00433
Ligands: HEM, CA
Pockets: 17 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Peroxidase C1A (EC 1.11.1.7)	protein	306	49% helix, 3% strand	P00433

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F

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

Pockets

17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	524	0.86	0.91	72	HEM
2	480	0.85	0.92	69	HEM
3	375	0.81	0.90	47	HEM
4	373	0.81	0.90	46	HEM
5	430	0.80	0.88	55	HEM

Interfaces

10 interfaces between chains.

A–D · 812 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 409 Å² buried · 5 hydrogen bonds · protein-protein
C–E · 399 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 389 Å² buried · 4 hydrogen bonds · protein-protein
A–F · 375 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

1ATJ · Recombinant horseradish peroxidase C1A · the same entry in another collection · chain C against C, 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 1ATJ · PDBe 1ATJ · UniProt P00433

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