MolNFT v1 · #103394 · protein

Crystal structure of engineered D-tagatose 3-epimerase pcdte-IDF8

4PFH: “Crystal structure of engineered D-tagatose 3-epimerase pcdte-IDF8”. X-ray diffraction, 3 ligands (PSJ, FUD, MN), 5 pockets (best druggability 0.73). MolNFT v1 #103394 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PFH
Type: protein
Length: 589 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-tagatose 3-epimerase
EC: 5.3.1.-
UniProt: O50580
Ligands: PSJ, FUD, MN
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-tagatose 3-epimerase (EC 5.3.1.-)	protein	298	45% helix, 15% strand	O50580
B	D-tagatose 3-epimerase (EC 5.3.1.-)	protein	291	46% helix, 16% strand	O50580

Ligands and binding sites

PSJ · D-psicose · ligand · 2 copies · chains A, B
FUD · D-fructose · ligand · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 3 copies · chains A, B

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

Pockets

5 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	69	0.73	0.98	22	PSJ, FUD
2	61	0.71	0.97	21	PSJ, FUD
3	281	0.56	0.77	50	empty
4	68	0.31	0.75	17	empty
5	57	0.31	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 1476 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

4PFH · Crystal structure of engineered D-tagatose 3-epimerase PcDTE-IDF8 · the same entry in another collection · chain A against A, TM-score 1.00
O50580 · AlphaFold monomer V2.0 prediction for D-tagatose 3-epimerase (O50580) · a predicted model of the same protein · chain B 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 O50580
Elsewhere: RCSB PDB 4PFH · PDBe 4PFH · UniProt O50580

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