Research workbench
Subsite mapping of the active site of human pancreatic alpha-amylase using substrates, the pharmacological inhibitor acarbose, and an active site variant
Analyse Subsite mapping of the active site of human pancreatic alpha-amylase using… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CPU
- Type
- protein
- Length
- 496 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (alpha-amylase)
- EC
- 3.2.1.1
- UniProt
- P04746
- Ligands
- AGL, HMC, GLC, NAG, CA, CL
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (alpha-amylase) (EC 3.2.1.1) | protein | 496 | 28% helix, 23% strand | P04746 |
Ligands and binding sites
- AGL · 4-amino-4,6-dideoxy-alpha-D-glucopyranose · ligand · chains A
- HMC · 5-hydroxymethyl-chonduritol · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · 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 | 235 | 0.56 | 0.78 | 26 | GLC, AGL, HMC |
| 2 | 80 | 0.37 | 0.77 | 20 | empty |
| 3 | 85 | 0.33 | 0.74 | 19 | empty |
| 4 | 53 | 0.29 | 0.75 | 13 | empty |
Modifications
Observed in the structure: 5 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 1CPU · Subsite mapping of the active site of human pancreatic alpha-amylase using substrates… · the same entry in another collection · chain A against A, TM-score 1.00
- P04746 · AlphaFold monomer V2.0 prediction for pancreatic alpha-amylase (P04746) · 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 P04746
- Elsewhere: RCSB PDB 1CPU · PDBe 1CPU · UniProt P04746
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