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Structure of helicobacter pylori catalase

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

PDB: 1QWL
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, OXY, AZI
Pockets: 16 · best druggability 0.79

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
OXY · Oxygen molecule · ion · chains A
AZI · Azide ion · ion · chains A, B

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

Pockets

16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	583	0.79	0.85	81	HEM, OXY
2	516	0.78	0.85	60	AZI, HEM
3	384	0.64	0.79	39	empty
4	411	0.64	0.78	34	empty
5	497	0.64	0.76	55	empty

Interfaces

1 interface between chains.

A–B · 2410 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

1QWL · Structure of Helicobacter pylori catalase · 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 1QWL · PDBe 1QWL · UniProt P77872

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