Research workbench
Vall from streptomyces hygroscopicus in complex with trehalose
Analyse Vall from streptomyces hygroscopicus in complex with trehalose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T7D
- Type
- protein
- Length
- 913 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glycosyltransferase
- UniProt
- Q15JG1
- Ligands
- GLC, MG
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative glycosyltransferase | protein | 459 | 47% helix, 19% strand | Q15JG1 |
| B | Putative glycosyltransferase | protein | 454 | 49% helix, 19% strand | Q15JG1 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- MG · Magnesium ion · metal · 18 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.81 | 0.83 | 73 | GLC, MG |
| 2 | 863 | 0.80 | 0.82 | 64 | GLC, MG |
| 3 | 159 | 0.63 | 0.85 | 25 | empty |
| 4 | 165 | 0.47 | 0.76 | 29 | MG |
| 5 | 139 | 0.45 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2134 Ų buried · 61 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3T7D · Vall from streptomyces hygroscopicus in complex with trehalose · 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 0.99
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 3T7D · PDBe 3T7D · UniProt Q15JG1
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