Research workbench

Monoclinic form of human peroxiredoxin 5

Analyse Monoclinic form of human peroxiredoxin 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1H4O
Type: protein
Length: 1,288 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxiredoxin 5
EC: 1.11.1.15
UniProt: P30044
Ligands: BEZ
Pockets: 13 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Peroxiredoxin 5 (EC 1.11.1.15)	protein	161	29% helix, 25% strand	P30044

Ligands and binding sites

BEZ · Benzoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	257	0.59	0.79	45	BEZ
2	293	0.58	0.78	52	BEZ
3	139	0.50	0.79	25	BEZ
4	104	0.50	0.81	20	BEZ
5	138	0.49	0.78	27	BEZ

Interfaces

6 interfaces between chains.

B–C · 465 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 459 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 450 Å² buried · 5 hydrogen bonds · protein-protein
F–G · 446 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 305 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1H4O · Monoclinic form of human peroxiredoxin 5 · the same entry in another collection · chain H against H, TM-score 1.00
P30044 · AlphaFold monomer V2.0 prediction for peroxiredoxin-5, mitochondrial (P30044) · 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 P30044
Elsewhere: RCSB PDB 1H4O · PDBe 1H4O · UniProt P30044

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