MolNFT v1 · #24107 · protein
Crystal structure of soybean beta-amylase mutant substituted at surface region
1UKP: “Crystal structure of soybean beta-amylase mutant substituted at surface region”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.75). MolNFT v1 #24107 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1UKP
- 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 0.75
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 · 20 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.75 | 0.82 | 58 | empty |
| 2 | 526 | 0.73 | 0.82 | 59 | empty |
| 3 | 578 | 0.72 | 0.80 | 52 | empty |
| 4 | 612 | 0.70 | 0.78 | 50 | empty |
| 5 | 635 | 0.70 | 0.78 | 52 | empty |
Interfaces
5 interfaces between chains.
- A–B · 560 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 494 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 493 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 302 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 230 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1UKP · 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 B 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 1UKP · PDBe 1UKP · UniProt P10538
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