MolNFT v1 · #26059 · protein
The role of an inner loop in the catalytic mechanism of soybean beta- amylase
1WDR · Beta-amylase: “The role of an inner loop in the catalytic mechanism of soybean beta- amylase”. X-ray diffraction, 2 ligands (GLC, SO4), 4 pockets (best druggability 0.75). MolNFT v1 #26059 on GenesisL1: 3D structure, binding sites…
- PDB
- 1WDR
- Type
- protein
- Length
- 493 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-amylase
- EC
- 3.2.1.2
- UniProt
- P10538
- Ligands
- GLC, SO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-amylase (EC 3.2.1.2) | protein | 493 | 39% helix, 12% strand | P10538 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 5 copies · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.75 | 0.85 | 55 | GLC |
| 2 | 124 | 0.55 | 0.83 | 37 | empty |
| 3 | 127 | 0.43 | 0.76 | 20 | empty |
| 4 | 65 | 0.35 | 0.78 | 18 | empty |
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 1WDR · The role of an inner loop in the catalytic mechanism of soybean beta-amylase · the same entry in another collection · chain A against A, TM-score 1.00
- P10538 · AlphaFold monomer V2.0 prediction for beta-amylase (P10538) · 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 P10538
- Elsewhere: RCSB PDB 1WDR · PDBe 1WDR · UniProt P10538
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