MolNFT v1 · #41159 · protein
Family 37 trehalase from escherichia COLI in complex with validoxylamine
2JF4 · Periplasmic trehalase: “Family 37 trehalase from escherichia COLI in complex with validoxylamine”. X-ray diffraction, 1 ligand (VDM), 3 pockets (best druggability 0.78). MolNFT v1 #41159 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2JF4
- Type
- protein
- Length
- 500 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic trehalase
- EC
- 3.2.1.28
- UniProt
- P13482
- Ligands
- VDM
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic trehalase (EC 3.2.1.28) | protein | 500 | 52% helix, 10% strand | P13482 |
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
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 | 105 | 0.78 | 0.97 | 25 | VDM |
| 2 | 53 | 0.36 | 0.79 | 11 | empty |
| 3 | 69 | 0.34 | 0.76 | 12 | empty |
Modifications
Observed in the structure: 14 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 2JF4 · Family 37 trehalase from Escherichia coli in complex with validoxylamine · the same entry in another collection · chain A against A, TM-score 1.00
- P13482 · AlphaFold monomer V2.0 prediction for periplasmic trehalase (P13482) · a predicted model of the same protein · 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 P13482
- Elsewhere: RCSB PDB 2JF4 · PDBe 2JF4 · UniProt P13482
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