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The structure of trehalose synthase (tres) of mycobacterium smegmatis in complex with acarbose
Analyse The structure of trehalose synthase (tres) of mycobacterium smegmatis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZOA
- Type
- protein
- Length
- 1,119 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trehalose SYNTHASE/AMYLASE tres
- EC
- 3.2.1.1, 5.4.99.16
- UniProt
- A0R6E0
- Ligands
- AC1, GLC, CA, MG, CL
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trehalose SYNTHASE/AMYLASE tres (EC 3.2.1.1, 5.4.99.16) | protein | 548 | 32% helix, 18% strand | A0R6E0 |
| B | Trehalose SYNTHASE/AMYLASE tres (EC 3.2.1.1, 5.4.99.16) | protein | 571 | 32% helix, 17% strand | A0R6E0 |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.84 | 0.85 | 77 | AC1 |
| 2 | 198 | 0.51 | 0.77 | 23 | empty |
| 3 | 186 | 0.49 | 0.76 | 24 | empty |
| 4 | 172 | 0.47 | 0.76 | 20 | empty |
| 5 | 115 | 0.45 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1019 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3ZOA · The structure of Trehalose Synthase (TreS) of Mycobacterium smegmatis in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- A0R6E0 · AlphaFold monomer V2.0 prediction for trehalose SYNTHASE/AMYLASE tres (A0R6E0) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 A0R6E0
- Elsewhere: RCSB PDB 3ZOA · PDBe 3ZOA · UniProt A0R6E0
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