MolNFT v1 · #141397 · protein
Structure of periplasmic trehalase from diamondback moth gut bacteria complexed with validoxylamine
5Z66: “Structure of periplasmic trehalase from diamondback moth gut bacteria complexed with validoxylamine”. X-ray diffraction, 2 ligands (VDM, SO4), 3 pockets (best druggability 0.77). MolNFT v1 #141397 on GenesisL1: 3D structure, binding…
- PDB
- 5Z66
- Type
- protein
- Length
- 512 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic trehalase
- EC
- 3.2.1.28
- UniProt
- A0A156C5X3
- Ligands
- VDM, SO4
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic trehalase (EC 3.2.1.28) | protein | 512 | 51% helix, 10% strand | A0A156C5X3 |
Ligands and binding sites
- VDM · (1S,2S,3R,6S)-4-(hydroxymethyl)-6-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}cyclohex-4-ene-1,2,3-triol · ligand · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A
- GOL · Glycerol · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.77 | 0.97 | 25 | VDM |
| 2 | 267 | 0.53 | 0.75 | 37 | empty |
| 3 | 97 | 0.38 | 0.75 | 15 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5Z66 · Structure of periplasmic trehalase from Diamondback moth gut bacteria complexed with… · 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 5Z66 · PDBe 5Z66 · UniProt A0A156C5X3
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