MolNFT v1 · #103432 · protein

Crystal structure of engineered D-tagatose 3-epimerase pcdte-ILS6

4PGL: “Crystal structure of engineered D-tagatose 3-epimerase pcdte-ILS6”. X-ray diffraction, 4 ligands (SOE, SOL, LTG), 12 pockets (best druggability 0.73). MolNFT v1 #103432 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PGL
Type: protein
Length: 1,176 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-tagatose 3-epimerase
EC: 5.3.1.-
UniProt: O50580
Ligands: SOE, SOL, LTG, MN
Pockets: 12 · best druggability 0.73

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	D-tagatose 3-epimerase (EC 5.3.1.-)	protein	298	46% helix, 15% strand	O50580
B, D	D-tagatose 3-epimerase (EC 5.3.1.-)	protein	290	46% helix, 16% strand	O50580

Ligands and binding sites

SOE · alpha-L-sorbopyranose · ligand · 5 copies · chains A, B, C, D
SOL · L-sorbose · ligand · 4 copies · chains A, B, C, D
LTG · L-tagatose · ligand · 4 copies · chains A, B, C, D
MN · Manganese (II) ion · metal · 5 copies · chains A, C, B, D

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	65	0.73	0.98	24	LTG, SOL
2	1071	0.71	0.75	89	SOE
3	67	0.70	0.96	22	LTG, SOL
4	122	0.64	0.87	32	LTG, SOL
5	254	0.63	0.81	45	SOL, LTG

Interfaces

3 interfaces between chains.

C–D · 1543 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 1532 Å² buried · 38 hydrogen bonds · protein-protein
A–C · 384 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4PGL · Crystal structure of engineered D-tagatose 3-epimerase PcDTE-ILS6 · the same entry in another collection · chain D against D, TM-score 1.00
O50580 · AlphaFold monomer V2.0 prediction for D-tagatose 3-epimerase (O50580) · a predicted model of the same protein · chain D against A, TM-score 1.00

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 4PGL · PDBe 4PGL · UniProt O50580

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