Research workbench
Crystal structure of vlde, the pseudo-glycosyltransferase which catalyzes non-glycosidic C-N coupling in validamycin a biosynthesis
Analyse Crystal structure of vlde, the pseudo-glycosyltransferase which catalyzes… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VDM
- Type
- protein
- Length
- 957 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vlde
- EC
- 2.4.-.-
- UniProt
- Q15JG1
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vlde (EC 2.4.-.-) | protein | 479 | 45% helix, 21% strand | Q15JG1 |
| B | Vlde (EC 2.4.-.-) | protein | 478 | 45% helix, 21% strand | Q15JG1 |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.76 | 0.78 | 71 | empty |
| 2 | 1058 | 0.75 | 0.77 | 71 | empty |
| 3 | 329 | 0.54 | 0.75 | 40 | empty |
| 4 | 185 | 0.49 | 0.76 | 34 | empty |
| 5 | 119 | 0.41 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 175 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3VDM · Crystal Structure of VldE, the pseudo-glycosyltransferase which catalyzes non-glycosidic… · the same entry in another collection · chain A against A, 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 3VDM · PDBe 3VDM · UniProt Q15JG1
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