Research workbench
Crystal structure of glycosyltransferase vinc in complex with dtdp
Analyse Crystal structure of glycosyltransferase vinc in complex with dtdp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WAG
- Type
- protein
- Length
- 800 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyltransferase
- UniProt
- Q76KZ6
- Ligands
- TYD, MG, PO4
- Pockets
- 10 · 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 | 399 | 49% helix, 14% strand | Q76KZ6 |
| B | Glycosyltransferase | protein | 401 | 49% helix, 14% strand | Q76KZ6 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.76 | 0.97 | 21 | PO4 |
| 2 | 72 | 0.74 | 0.97 | 19 | PO4 |
| 3 | 658 | 0.70 | 0.78 | 63 | TYD |
| 4 | 523 | 0.68 | 0.78 | 58 | TYD |
| 5 | 186 | 0.57 | 0.81 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 1638 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3WAG · Crystal structure of glycosyltransferase VinC in complex with DTDP · 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 3WAG · PDBe 3WAG · UniProt Q76KZ6
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