Research workbench
Crystal structure of vlde, the pseudo-glycosyltransferase, in complex with GDP and trehalose
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
- 4F9F
- Type
- protein
- Length
- 2,780 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vlde
- EC
- 2.4.-.-
- UniProt
- Q15JG1
- Ligands
- GDP, GLC
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vlde (EC 2.4.-.-) | protein | 470 | 45% helix, 21% strand | Q15JG1 |
| B | Vlde (EC 2.4.-.-) | protein | 463 | 45% helix, 20% strand | Q15JG1 |
| C | Vlde (EC 2.4.-.-) | protein | 460 | 47% helix, 20% strand | Q15JG1 |
| D | Vlde (EC 2.4.-.-) | protein | 464 | 45% helix, 20% strand | Q15JG1 |
| E | Vlde (EC 2.4.-.-) | protein | 463 | 47% helix, 20% strand | Q15JG1 |
| F | Vlde (EC 2.4.-.-) | protein | 460 | 47% helix, 20% strand | Q15JG1 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.84 | 0.89 | 64 | GDP |
| 2 | 656 | 0.84 | 0.88 | 73 | GDP |
| 3 | 461 | 0.83 | 0.90 | 56 | GDP |
| 4 | 634 | 0.82 | 0.87 | 69 | GDP |
| 5 | 1095 | 0.80 | 0.82 | 85 | empty |
Interfaces
10 interfaces between chains.
- C–F · 2223 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2187 Ų buried · 57 hydrogen bonds · protein-protein
- D–E · 2183 Ų buried · 55 hydrogen bonds · protein-protein
- A–F · 565 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 508 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4F9F · Crystal Structure of VldE, the pseudo-glycosyltransferase, in complex with GDP and… · the same entry in another collection · chain F against F, TM-score 1.00
- Q15JG1 · AlphaFold monomer V2.0 prediction for validamine 7-phosphate valienyltransferase (Q15JG1) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 4F9F · PDBe 4F9F · UniProt Q15JG1
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