Research workbench
Crystal structure of soybean beta-amylase mutant substituted at surface region
Analyse Crystal structure of soybean beta-amylase mutant substituted at surface region in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UKO
- Type
- protein
- Length
- 1,960 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-amylase
- EC
- 3.2.1.2
- UniProt
- P10538
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-amylase (EC 3.2.1.2) | protein | 490 | 40% helix, 12% strand | P10538 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 24 copies · chains A, B, C, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.78 | 0.80 | 93 | SO4 |
| 2 | 564 | 0.73 | 0.81 | 57 | empty |
| 3 | 595 | 0.73 | 0.80 | 90 | empty |
| 4 | 635 | 0.71 | 0.78 | 53 | SO4 |
| 5 | 449 | 0.71 | 0.81 | 49 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 543 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 521 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 519 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 332 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 262 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1UKO · Crystal structure of soybean beta-amylase mutant substituted at surface region · the same entry in another collection · chain D against D, TM-score 1.00
- P10538 · AlphaFold monomer V2.0 prediction for beta-amylase (P10538) · 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 P10538
- Elsewhere: RCSB PDB 1UKO · PDBe 1UKO · UniProt P10538
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