MolNFT v1 · #14570 · protein

Mandelate racemase mutant K166R co-crystallized with (R)-mandelate

1MDL: “Mandelate racemase mutant K166R co-crystallized with (R)-mandelate”. X-ray diffraction, 3 ligands (RMN, SMN, MG), 2 pockets (best druggability 0.65). MolNFT v1 #14570 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1MDL
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: RMN, SMN, MG
Pockets: 2 · best druggability 0.65

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

RMN · (R)-mandelic acid · ligand · chains A
SMN · (S)-mandelic 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

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	246	0.65	0.83	38	RMN, SMN
2	55	0.34	0.78	15	empty

Compared structures

1MDL · Mandelate racemase mutant K166R co-crystallized with (R)-mandelate · 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 1MDL · PDBe 1MDL · UniProt P11444

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