MolNFT v1 · #109437 · protein

P. putida mandelate racemase in complex with 3-hydroxypyruvate

4X2P: “P. putida mandelate racemase in complex with 3-hydroxypyruvate”. X-ray diffraction, 2 ligands (3PY, MG), 1 pocket (best druggability 0.63). MolNFT v1 #109437 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4X2P
Type: protein
Length: 357 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mandelate racemase
EC: 5.1.2.2
UniProt: P11444
Ligands: 3PY, MG
Pockets: 1 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mandelate racemase (EC 5.1.2.2)	protein	357	41% helix, 23% strand	P11444

Ligands and binding sites

3PY · 3-hydroxypyruvic acid · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	364	0.63	0.78	43	3PY

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

4X2P · P. putida mandelate racemase in complex with 3-hydroxypyruvate · the same entry in another collection · chain A against A, TM-score 1.00
P11444 · AlphaFold monomer V2.0 prediction for mandelate racemase (P11444) · 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 P11444
Elsewhere: RCSB PDB 4X2P · PDBe 4X2P · UniProt P11444

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