MolNFT v1 · #51900 · protein

Oxidized and reduced forms of human peroxiredoxin 5

2VL3 · Peroxiredoxin-5: “Oxidized and reduced forms of human peroxiredoxin 5”. X-ray diffraction, 3 pockets (best druggability 0.63). MolNFT v1 #51900 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VL3
Type: protein
Length: 484 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxiredoxin-5
EC: 1.11.1.15
UniProt: P30044
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxiredoxin-5 (EC 1.11.1.15)	protein	162	31% helix, 25% strand	P30044
B, C	Peroxiredoxin-5 (EC 1.11.1.15)	protein	161	30% helix, 24% strand	P30044

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	319	0.63	0.79	42	empty
2	110	0.45	0.78	21	empty
3	96	0.37	0.75	23	empty

Interfaces

2 interfaces between chains.

B–C · 808 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 450 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

2VL3 · Oxidized and reduced forms of human peroxiredoxin 5 · the same entry in another collection · chain A against A, 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 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 P30044
Elsewhere: RCSB PDB 2VL3 · PDBe 2VL3 · UniProt P30044

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