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Crystal structure of human erythrocyte catalase

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

PDB: 1QQW
Type: protein
Length: 1,997 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catalase
EC: 1.11.1.6
UniProt: P04040
Ligands: HEM
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Catalase (EC 1.11.1.6)	protein	499	33% helix, 18% strand	P04040
B	Catalase (EC 1.11.1.6)	protein	500	33% helix, 18% strand	P04040

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, D, B, C

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	427	0.87	0.96	51	empty
2	725	0.87	0.91	53	empty
3	426	0.87	0.95	54	empty
4	318	0.86	0.95	45	HEM
5	310	0.85	0.95	45	HEM

Interfaces

6 interfaces between chains.

A–D · 4921 Å² buried · 77 hydrogen bonds · protein-protein
B–C · 4918 Å² buried · 87 hydrogen bonds · protein-protein
A–C · 4683 Å² buried · 47 hydrogen bonds · protein-protein
B–D · 4641 Å² buried · 44 hydrogen bonds · protein-protein
C–D · 2053 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

1QQW · Crystal structure of human erythrocyte catalase · the same entry in another collection · chain D against D, TM-score 1.00
P04040 · AlphaFold monomer V2.0 prediction for catalase (P04040) · a predicted model of the same protein · chain C 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 P04040
Elsewhere: RCSB PDB 1QQW · PDBe 1QQW · UniProt P04040

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