MolNFT v1 · #16885 · protein

Human peroxiredoxin 5

1OC3: “Human peroxiredoxin 5”. X-ray diffraction, 1 ligand (BEZ), 3 pockets (best druggability 0.45). MolNFT v1 #16885 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1OC3
Type: protein
Length: 484 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxiredoxin 5
UniProt: P30044
Ligands: BEZ
Pockets: 3 · best druggability 0.45

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peroxiredoxin 5	protein	162	30% helix, 25% strand	P30044
B, C	Peroxiredoxin 5	protein	161	31% helix, 25% 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

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	103	0.45	0.78	18	BEZ
2	102	0.38	0.76	21	empty
3	52	0.27	0.74	13	empty

Interfaces

2 interfaces between chains.

B–C · 964 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 459 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1OC3 · 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 1OC3 · PDBe 1OC3 · UniProt P30044

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