MolNFT v1 · #51899 · protein

Oxidized and reduced forms of human peroxiredoxin 5

2VL2 · Peroxiredoxin-5: “Oxidized and reduced forms of human peroxiredoxin 5”. X-ray diffraction, 1 ligand (BEZ), 6 pockets (best druggability 0.53). MolNFT v1 #51899 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VL2
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
Ligands: BEZ
Pockets: 6 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxiredoxin-5 (EC 1.11.1.15)	protein	162	32% helix, 25% strand	P30044
B, C	Peroxiredoxin-5 (EC 1.11.1.15)	protein	161	32% helix, 24% strand	P30044

Ligands and binding sites

BEZ · Benzoic acid · ligand · 2 copies · chains A, C, B

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	231	0.53	0.76	25	empty
2	95	0.51	0.83	23	empty
3	129	0.46	0.77	27	BEZ
4	60	0.31	0.76	18	empty
5	52	0.30	0.76	12	empty

Interfaces

2 interfaces between chains.

B–C · 798 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 449 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2VL2 · 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 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 P30044
Elsewhere: RCSB PDB 2VL2 · PDBe 2VL2 · UniProt P30044

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