MolNFT v1 · #141406 · protein
Structure of periplasmic trehalase from diamondback moth gut bacteria in the apo form
5Z6H: “Structure of periplasmic trehalase from diamondback moth gut bacteria in the apo form”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.71). MolNFT v1 #141406 on GenesisL1: 3D structure, binding sites and pockets…
- 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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