MolNFT v1 · #100072 · protein

Human PDRX5 complex with a ligand BP7

4MMM · Peroxiredoxin-5, mitochondrial: “Human PDRX5 complex with a ligand BP7”. X-ray diffraction, 1 ligand (BP7), 5 pockets (best druggability 0.68). MolNFT v1 #100072 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4MMM
Type: protein
Length: 648 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxiredoxin-5, mitochondrial
EC: 1.11.1.15
UniProt: P30044
Ligands: BP7
Pockets: 5 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Peroxiredoxin-5, mitochondrial (EC 1.11.1.15)	protein	162	33% helix, 25% strand	P30044

Ligands and binding sites

BP7 · 1,1'-biphenyl-3,4-diol · ligand · 2 copies · chains A, E, C, G

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

Pockets

5 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	453	0.68	0.79	58	BP7
2	183	0.53	0.78	20	empty
3	78	0.36	0.76	20	empty
4	84	0.34	0.75	19	empty
5	53	0.29	0.75	13	empty

Interfaces

4 interfaces between chains.

C–G · 795 Å² buried · 2 hydrogen bonds · protein-protein
A–E · 782 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 370 Å² buried · 2 hydrogen bonds · protein-protein
A–G · 10 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4MMM · Human Pdrx5 complex with a ligand BP7 · 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 4MMM · PDBe 4MMM · UniProt P30044

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