Research workbench

P. putida mandelate racemase co-crystallized with 3,3,3-trifluoro-2- hydroxy-2-(trifluoromethyl) propionic acid

Analyse P. putida mandelate racemase co-crystallized with 3,3,3-trifluoro-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FP1
Type: protein
Length: 714 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mandelate racemase
EC: 5.1.2.2
UniProt: P11444
Ligands: BFM, MG
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Mandelate racemase (EC 5.1.2.2)	protein	357	40% helix, 22% strand	P11444

Ligands and binding sites

BFM · 3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl)propanoic acid · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	85	0.74	0.97	22	BFM
2	74	0.73	0.97	18	BFM
3	538	0.71	0.80	70	empty
4	140	0.48	0.78	21	empty
5	101	0.48	0.81	18	empty

Interfaces

1 interface between chains.

A–B · 1506 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4FP1 · P. putida mandelate racemase co-crystallized with… · 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 4FP1 · PDBe 4FP1 · UniProt P11444

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.