MolNFT v1 · #51906 · protein

Oxidized form of human peroxiredoxin 5

2VL9 · Peroxiredoxin-5: “Oxidized form of human peroxiredoxin 5”. X-ray diffraction, 7 pockets (best druggability 0.77). MolNFT v1 #51906 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VL9
Type: protein
Length: 644 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxiredoxin-5
EC: 1.11.1.15
UniProt: P30044
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Peroxiredoxin-5 (EC 1.11.1.15)	protein	161	16% helix, 13% strand	P30044

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1054	0.77	0.79	83	empty
2	135	0.62	0.85	29	empty
3	104	0.59	0.86	23	empty
4	212	0.54	0.77	21	empty
5	148	0.46	0.76	24	empty

Interfaces

6 interfaces between chains.

A–C · 809 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 738 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 220 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 190 Å² buried · 1 hydrogen bond · protein-protein
B–D · 39 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2VL9 · Oxidized form 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 0.92

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 2VL9 · PDBe 2VL9 · UniProt P30044

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