Research workbench
Structure of pig pancreatic alpha-amylase complexed with the "truncate" acarbose molecule (pseudotrisaccharide)
Analyse Structure of pig pancreatic alpha-amylase complexed with the "truncate"… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HX0
- Type
- protein
- Length
- 496 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha amylase (ppa)
- EC
- 3.2.1.1
- UniProt
- P00690
- Ligands
- AC1, GLC, CA, CL
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha amylase (ppa) (EC 3.2.1.1) | protein | 496 | 28% helix, 24% strand | P00690 |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · 2 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 12 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.61 | 0.80 | 24 | GLC, AC1 |
| 2 | 78 | 0.42 | 0.79 | 12 | empty |
| 3 | 98 | 0.41 | 0.78 | 21 | EDO |
| 4 | 68 | 0.31 | 0.75 | 15 | empty |
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 1HX0 · Structure of pig pancreatic alpha-amylase complexed with the "truncate" acarbose molecule… · the same entry in another collection · chain A against A, TM-score 1.00
- P00690 · AlphaFold monomer V2.0 prediction for pancreatic alpha-amylase (P00690) · 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 P00690
- Elsewhere: RCSB PDB 1HX0 · PDBe 1HX0 · UniProt P00690
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