MolNFT v2 · #124421 · protein
Structure of Mycobacterium thermoresistibile trehalose-6-phosphate synthase in a complex with GDP-glucose.
5K42 · Alpha,alpha-trehalose-phosphate synthase: “Structure of Mycobacterium thermoresistibile trehalose-6-phosphate synthase in a complex with GDP-glucose.”. X-ray diffraction at 1.921, 1 ligand (GDG), 3 pockets (best druggability 0.74).…
- PDB
- 5K42
- Type
- protein
- Length
- 461 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.921
- Source
- Mycobacterium thermoresistibile
- Molecule
- Alpha,alpha-trehalose-phosphate synthase
- UniProt
- A0A117IMA6
- Ligands
- GDG
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.921 · 1 distinct chain · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha,alpha-trehalose-phosphate synthase | protein | 461 | 46% helix, 21% strand | A0A117IMA6 |
Ligands and binding sites
- GDG · Gdp-alpha-D-glucose · ligand · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.74 | 0.77 | 61 | GDG |
| 2 | 78 | 0.44 | 0.81 | 21 | empty |
| 3 | 50 | 0.30 | 0.76 | 13 | empty |
Compared structures
- 5K42 · Structure of mycobacterium thermoresistibile trehalose-6-phosphate synthase in a complex… · 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 A0A117IMA6
- Elsewhere: RCSB PDB 5K42 · PDBe 5K42 · UniProt A0A117IMA6
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