MolNFT v1 · #54474 · protein

Crystal structure of peroxisomal catalase from the yeast hansenula polymorpha

2XQ1: “Crystal structure of peroxisomal catalase from the yeast hansenula polymorpha”. X-ray diffraction, 1 ligand (HEM), 20 pockets (best druggability 0.88). MolNFT v1 #54474 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2XQ1
Type: protein
Length: 7,860 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxisomal catalase
EC: 1.11.1.6
UniProt: P30263
Ligands: HEM
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 12 distinct chains · 32% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I	Peroxisomal catalase (EC 1.11.1.6)	protein	491	32% helix, 19% strand	P30263
B, D, F	Peroxisomal catalase (EC 1.11.1.6)	protein	494	32% helix, 19% strand	P30263
C	Peroxisomal catalase (EC 1.11.1.6)	protein	492	32% helix, 19% strand	P30263
E	Peroxisomal catalase (EC 1.11.1.6)	protein	490	32% helix, 19% strand	P30263
G, P	Peroxisomal catalase (EC 1.11.1.6)	protein	491	32% helix, 19% strand	P30263
H	Peroxisomal catalase (EC 1.11.1.6)	protein	487	33% helix, 19% strand	P30263
J	Peroxisomal catalase (EC 1.11.1.6)	protein	491	33% helix, 19% strand	P30263
K	Peroxisomal catalase (EC 1.11.1.6)	protein	490	33% helix, 19% strand	P30263
L	Peroxisomal catalase (EC 1.11.1.6)	protein	489	33% helix, 19% strand	P30263
M	Peroxisomal catalase (EC 1.11.1.6)	protein	491	32% helix, 19% strand	P30263
N	Peroxisomal catalase (EC 1.11.1.6)	protein	491	32% helix, 19% strand	P30263
O	Peroxisomal catalase (EC 1.11.1.6)	protein	493	31% helix, 19% strand	P30263

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 15 copies · chains B, C, A, D, E, H, F, G, I, L, J, K, M, P, N, O

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	699	0.88	0.92	52	empty
2	716	0.88	0.92	52	empty
3	708	0.87	0.91	53	empty
4	709	0.87	0.91	55	empty
5	273	0.85	0.96	40	empty

Interfaces

37 interfaces between chains.

J–K · 4988 Å² buried · 52 hydrogen bonds · protein-protein
M–P · 4982 Å² buried · 52 hydrogen bonds · protein-protein
N–O · 4981 Å² buried · 49 hydrogen bonds · protein-protein
B–C · 4968 Å² buried · 50 hydrogen bonds · protein-protein
F–G · 4965 Å² buried · 51 hydrogen bonds · protein-protein

Compared structures

2XQ1 · Crystal structure of peroxisomal catalase from the yeast Hansenula polymorpha · the same entry in another collection · chain K against K, 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 P30263
Elsewhere: RCSB PDB 2XQ1 · PDBe 2XQ1 · UniProt P30263

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