Research workbench
Structure of periplasmic trehalase from diamondback moth gut bacteria in the apo form
Analyse Structure of periplasmic trehalase from diamondback moth gut bacteria in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z6H
- Type
- protein
- Length
- 1,008 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic trehalase
- EC
- 3.2.1.28
- UniProt
- A0A156C5X3
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic trehalase (EC 3.2.1.28) | protein | 505 | 50% helix, 8% strand | A0A156C5X3 |
| B | Periplasmic trehalase (EC 3.2.1.28) | protein | 503 | 52% helix, 9% strand | A0A156C5X3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.71 | 0.80 | 37 | GOL |
| 2 | 514 | 0.69 | 0.79 | 41 | GOL |
| 3 | 898 | 0.68 | 0.74 | 87 | SO4 |
| 4 | 604 | 0.67 | 0.77 | 58 | empty |
| 5 | 142 | 0.41 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 703 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5Z6H · Structure of periplasmic trehalase from Diamondback moth gut bacteria in the apo form · 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 A0A156C5X3
- Elsewhere: RCSB PDB 5Z6H · PDBe 5Z6H · UniProt A0A156C5X3
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