Research workbench

Thioredoxin peroxidase from aeropyrum pernix K1

Analyse Thioredoxin peroxidase from aeropyrum pernix K1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1X0R
Type: protein
Length: 2,440 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable peroxiredoxin
EC: 1.11.1.15
UniProt: Q9Y9L0
Pockets: 19 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Probable peroxiredoxin (EC 1.11.1.15)	protein	244	36% helix, 24% strand	Q9Y9L0

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 128 copies · chains A, B, I, C, J, D, E, F, G, H

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

Pockets

19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	283	0.57	0.77	44	EDO
2	306	0.56	0.76	42	EDO
3	312	0.56	0.76	43	EDO
4	277	0.55	0.76	41	EDO
5	245	0.55	0.77	41	EDO

Interfaces

20 interfaces between chains.

E–F · 3596 Å² buried · 56 hydrogen bonds · protein-protein
A–B · 3556 Å² buried · 53 hydrogen bonds · protein-protein
C–D · 3552 Å² buried · 60 hydrogen bonds · protein-protein
G–H · 3528 Å² buried · 53 hydrogen bonds · protein-protein
I–J · 3504 Å² buried · 56 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 40 modified (engineered).

Compared structures

1X0R · Thioredoxin Peroxidase from Aeropyrum pernix K1 · the same entry in another collection · chain J against J, TM-score 1.00
Q9Y9L0 · AlphaFold monomer V2.0 prediction for peroxiredoxin (Q9Y9L0) · 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 Q9Y9L0
Elsewhere: RCSB PDB 1X0R · PDBe 1X0R · UniProt Q9Y9L0

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