Research workbench
Crystal structure of vlde, the pseudo-glycosyltransferase, in complex with GDP
Analyse Crystal structure of vlde, the pseudo-glycosyltransferase, in complex with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F96
- Type
- protein
- Length
- 944 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vlde
- EC
- 2.4.-.-
- UniProt
- Q15JG1
- Ligands
- GDP, CL
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Vlde (EC 2.4.-.-) | protein | 472 | 46% helix, 21% strand | Q15JG1 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, A
- CL · Chloride ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.72 | 0.77 | 60 | GDP |
| 2 | 877 | 0.71 | 0.76 | 62 | GDP |
| 3 | 184 | 0.63 | 0.84 | 26 | empty |
| 4 | 332 | 0.55 | 0.75 | 58 | empty |
| 5 | 60 | 0.35 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 2159 Ų buried · 60 hydrogen bonds · protein-protein
Compared structures
- 4F96 · Crystal Structure of VldE, the pseudo-glycosyltransferase, in complex with GDP · the same entry in another collection · chain B against B, TM-score 1.00
- Q15JG1 · AlphaFold monomer V2.0 prediction for validamine 7-phosphate valienyltransferase (Q15JG1) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q15JG1
- Elsewhere: RCSB PDB 4F96 · PDBe 4F96 · UniProt Q15JG1
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