MolNFT v1 · #104338 · protein

Crystal structure of engineered thermostable D-tagatose 3-epimerase pcdte-VAR8

4Q7I: “Crystal structure of engineered thermostable D-tagatose 3-epimerase pcdte-VAR8”. X-ray diffraction, 1 ligand (MN), 5 pockets (best druggability 0.63). MolNFT v1 #104338 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Q7I
Type: protein
Length: 588 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-tagatose 3-epimerase
Ligands: MN
Pockets: 5 · best druggability 0.63

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-tagatose 3-epimerase	protein	298	46% helix, 15% strand	—
B	D-tagatose 3-epimerase	protein	290	46% helix, 16% strand	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B
IMD · Imidazole · additive · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	235	0.63	0.82	42	GOL, IMD
2	150	0.63	0.85	31	GOL
3	80	0.33	0.74	16	empty
4	79	0.30	0.73	17	empty
5	66	0.28	0.73	16	empty

Interfaces

1 interface between chains.

A–B · 1553 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

4Q7I · Crystal structure of engineered thermostable D-tagatose 3-epimerase PcDTE-Var8 · the same entry in another collection · chain A 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
Elsewhere: RCSB PDB 4Q7I · PDBe 4Q7I

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