Research workbench
Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 ångström resolution
Analyse Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JFH
- Type
- protein
- Length
- 496 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.03
- Source
- Sus scrofa
- Molecule
- Alpha-amylase
- EC
- 3.2.1.1
- UniProt
- P00690
- Ligands
- MA1, GLC, MA3, MA2, HG, CA, CL
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · resolution 2.03 · 1 distinct chain · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-amylase (EC 3.2.1.1) | protein | 496 | 28% helix, 24% strand | P00690 |
Ligands and binding sites
- MA1 · 1,4-dithio-alpha-D-glucopyranose · sugar · 2 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- MA3 · methyl 4-thio-alpha-D-glucopyranoside · sugar · chains A
- MA2 · 4-S-methyl-4-thio-alpha-D-glucopyranose · sugar · chains A
- HG · Mercury (II) ion · metal · 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 | 248 | 0.61 | 0.80 | 23 | MA3, MA1, GLC |
| 2 | 80 | 0.37 | 0.77 | 19 | empty |
| 3 | 53 | 0.34 | 0.78 | 11 | empty |
| 4 | 76 | 0.32 | 0.75 | 19 | empty |
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 1JFH · Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 ångström… · 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 1JFH · PDBe 1JFH · UniProt P00690
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