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Crystal structure of glycosyltransferase vinc involved in the biosynthesis of vicenistatin

Analyse Crystal structure of glycosyltransferase vinc involved in the biosynthesis of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WAD
Type: protein
Length: 799 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycosyltransferase
UniProt: Q76KZ6
Ligands: MG
Pockets: 8 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycosyltransferase	protein	398	49% helix, 14% strand	Q76KZ6
B	Glycosyltransferase	protein	401	49% helix, 14% strand	Q76KZ6

Ligands and binding sites

MG · Magnesium ion · metal · chains A

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	621	0.76	0.82	76	empty
2	82	0.75	0.97	22	empty
3	657	0.69	0.77	61	empty
4	175	0.56	0.80	31	empty
5	108	0.52	0.82	30	empty

Interfaces

1 interface between chains.

A–B · 1670 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

3WAD · Crystal structure of glycosyltransferase VinC involved in the biosynthesis of vicenistatin · 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
Every structure of UniProt Q76KZ6
Elsewhere: RCSB PDB 3WAD · PDBe 3WAD · UniProt Q76KZ6

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