Research workbench

Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys W211A mutant

Analyse Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys W211A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KRS
Type: protein
Length: 2,420 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.3
Source: Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
Molecule: Peroxiredoxin
EC: 1.11.1.15
UniProt: Q9Y9L0
Pockets: 20 · best druggability 0.66

Structure

x-ray diffraction · resolution 2.3 · 1 distinct chain · 36% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Peroxiredoxin (EC 1.11.1.15)	protein	242	36% helix, 23% strand	Q9Y9L0

Ligands and binding sites

CIT · Citric acid · additive · 10 copies · chains A, B, E, H, C, D, F, I, G, J

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	85	0.66	0.91	18	empty
2	104	0.63	0.88	20	empty
3	81	0.59	0.88	18	empty
4	55	0.58	0.90	17	empty
5	109	0.58	0.85	23	empty

Interfaces

20 interfaces between chains.

G–H · 3293 Å² buried · 44 hydrogen bonds · protein-protein
I–J · 3279 Å² buried · 46 hydrogen bonds · protein-protein
A–B · 3239 Å² buried · 42 hydrogen bonds · protein-protein
E–F · 3229 Å² buried · 46 hydrogen bonds · protein-protein
C–D · 3211 Å² buried · 45 hydrogen bonds · protein-protein

Compared structures

6KRS · Peroxiredoxin from aeropyrum pernix K1 (apprx) 0CYS W211A mutant · 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 0.99

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 6KRS · PDBe 6KRS · UniProt Q9Y9L0

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