Research workbench

Helicobacter pylori catalase compound I

Analyse Helicobacter pylori catalase compound I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2A9E
Type: protein
Length: 982 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kata catalase
EC: 1.11.1.6
UniProt: P77872
Ligands: HEM, O
Pockets: 17 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Kata catalase (EC 1.11.1.6)	protein	491	34% helix, 17% strand	P77872

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
O · Oxygen atom · ion · 2 copies · chains A, B
ACT · Acetate ion · additive · chains A, B

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

Pockets

17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1134	0.84	0.85	128	ACT, HEM, O
2	405	0.64	0.78	37	empty
3	381	0.64	0.79	32	empty
4	423	0.61	0.76	43	empty
5	366	0.60	0.77	34	empty

Interfaces

1 interface between chains.

A–B · 2434 Å² buried · 40 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (oxidation).

Compared structures

2A9E · Helicobacter pylori catalase compound I · the same entry in another collection · chain A against A, TM-score 1.00
P77872 · AlphaFold monomer V2.0 prediction for catalase (P77872) · a predicted model of the same protein · chain B 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 P77872
Elsewhere: RCSB PDB 2A9E · PDBe 2A9E · UniProt P77872

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