Research workbench
Structure of porcine pancreatic alpha-amylase
Analyse Structure of porcine pancreatic alpha-amylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DHK
- Type
- protein
- Length
- 691 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Porcine pancreatic alpha-amylase; Bean lectin-like inhibitor
- EC
- 3.2.1.1
- UniProt
- P00690, P02873
- Ligands
- NAG, CA, CL
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Porcine pancreatic alpha-amylase (EC 3.2.1.1) | protein | 496 | 27% helix, 24% strand | P00690 |
| B | Bean lectin-like inhibitor | protein | 195 | 6% helix, 56% strand | P02873 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B
- CA · Calcium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.59 | 0.87 | 22 | empty |
| 2 | 208 | 0.55 | 0.79 | 28 | empty |
| 3 | 82 | 0.38 | 0.77 | 18 | empty |
| 4 | 67 | 0.35 | 0.77 | 12 | empty |
| 5 | 79 | 0.32 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1615 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 3 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 1DHK · Structure of porcine pancreatic alpha-amylase · the same entry in another collection · chain A against A, TM-score 1.00
- P02873 · AlphaFold monomer V2.0 prediction for alpha-amylase inhibitor 1 (P02873) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P00690 · AlphaFold monomer V2.0 prediction for pancreatic alpha-amylase (P00690) · a predicted model of the same protein · chain A 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 P00690
- Every structure of UniProt P02873
- Elsewhere: RCSB PDB 1DHK · PDBe 1DHK · UniProt P00690 · UniProt P02873
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