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Peroxiredoxin from pyrococcus horikoshii (sulfonic acid form)

Analyse Peroxiredoxin from pyrococcus horikoshii (sulfonic acid form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XBR
Type: protein
Length: 421 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxiredoxin
EC: 1.11.1.15
UniProt: O58966
Pockets: 3 · best druggability 0.33

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxiredoxin (EC 1.11.1.15)	protein	211	33% helix, 27% strand	O58966
B	Peroxiredoxin (EC 1.11.1.15)	protein	210	35% helix, 27% strand	O58966

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	66	0.33	0.76	15	GOL
2	55	0.30	0.75	16	GOL
3	67	0.28	0.73	15	empty

Interfaces

1 interface between chains.

A–B · 2428 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified, 1 disulfide (oxidation, disulfide).

Compared structures

5XBR · Peroxiredoxin from Pyrococcus horikoshii (sulfonic acid form) · the same entry in another collection · chain A against A, TM-score 1.00
O58966 · AlphaFold monomer V2.0 prediction for peroxiredoxin (O58966) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 O58966
Elsewhere: RCSB PDB 5XBR · PDBe 5XBR · UniProt O58966

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