Research workbench

Peroxiredoxin (C50S) from aeropytum pernix K1 (peroxide-bound form)

Analyse Peroxiredoxin (C50S) from aeropytum pernix K1 (peroxide-bound form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3A2W
Type: protein
Length: 2,437 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
Ligands: PER
Pockets: 20 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, F, H, I, J	Probable peroxiredoxin (EC 1.11.1.15)	protein	244	36% helix, 24% strand	Q9Y9L0
C, E, G	Probable peroxiredoxin (EC 1.11.1.15)	protein	243	36% helix, 24% strand	Q9Y9L0

Ligands and binding sites

PER · Peroxide ion · ion · 3 copies · chains B, F, I
GOL · Glycerol · additive · 7 copies · chains A, B, C, D, E, F, G, H, I, 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, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	363	0.58	0.76	41	GOL
2	337	0.58	0.76	40	GOL
3	333	0.57	0.76	44	PER
4	307	0.56	0.76	41	GOL
5	319	0.56	0.75	39	PER

Interfaces

20 interfaces between chains.

E–F · 3582 Å² buried · 55 hydrogen bonds · protein-protein
G–H · 3522 Å² buried · 56 hydrogen bonds · protein-protein
I–J · 3518 Å² buried · 60 hydrogen bonds · protein-protein
A–B · 3509 Å² buried · 51 hydrogen bonds · protein-protein
C–D · 3479 Å² buried · 54 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

3A2W · Peroxiredoxin (C50S) from Aeropytum pernix K1 (peroxide-bound form) · 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 C 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 3A2W · PDBe 3A2W · UniProt Q9Y9L0

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