MolNFT v1 · #53569 · protein
Structure of family 37 trehalase from escherichia COLI in complex with a casuarine-6-O-a-D-glucoside analogue
2WYN · Periplasmic trehalase: “Structure of family 37 trehalase from escherichia COLI in complex with a casuarine-6-O-a-D-glucoside analogue”. X-ray diffraction, 4 ligands (LG9, GLC, CA), 20 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 2WYN
- Type
- protein
- Length
- 2,013 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic trehalase
- EC
- 3.2.1.28
- UniProt
- P13482
- Ligands
- LG9, GLC, CA, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic trehalase (EC 3.2.1.28) | protein | 506 | 52% helix, 9% strand | P13482 |
| B | Periplasmic trehalase (EC 3.2.1.28) | protein | 503 | 52% helix, 10% strand | P13482 |
| C | Periplasmic trehalase (EC 3.2.1.28) | protein | 501 | 51% helix, 9% strand | P13482 |
| D | Periplasmic trehalase (EC 3.2.1.28) | protein | 503 | 52% helix, 10% strand | P13482 |
Ligands and binding sites
- LG9 · (1r,2r,3r,6r,7r,7ar)-3,7-bis(hydroxymethyl)hexahydro-1H-pyrrolizine-1,2,6-triol · ligand · 4 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 32 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.85 | 0.89 | 92 | SO4 |
| 2 | 874 | 0.81 | 0.84 | 73 | SO4 |
| 3 | 246 | 0.79 | 0.92 | 38 | LG9, GLC, SO4 |
| 4 | 259 | 0.73 | 0.87 | 35 | LG9, GLC, SO4 |
| 5 | 241 | 0.73 | 0.87 | 33 | LG9, GLC, SO4 |
Interfaces
5 interfaces between chains.
- B–D · 2496 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 2196 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 336 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 171 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 72 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2WYN · Structure of family 37 trehalase from Escherichia coli in complex with a… · the same entry in another collection · chain D against D, TM-score 1.00
- P13482 · AlphaFold monomer V2.0 prediction for periplasmic trehalase (P13482) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 2WYN · PDBe 2WYN · UniProt P13482
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