MolNFT v1 · #67398 · protein
Directed 'in situ' elongation as a strategy to characterize the covalent glycosyl-enzyme catalytic intermediate of human pancreatic a-amylase
3IJ9 · Pancreatic alpha-amylase: “Directed 'in situ' elongation as a strategy to characterize the covalent glycosyl-enzyme catalytic…”. X-ray diffraction, 5 ligands (B0D, B9D, BGC), 3 pockets (best druggability 0.57). MolNFT v1 #67398 on…
- PDB
- 3IJ9
- Type
- protein
- Length
- 496 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pancreatic alpha-amylase
- EC
- 3.2.1.1
- UniProt
- P04746
- Ligands
- B0D, B9D, BGC, CA, CL
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pancreatic alpha-amylase (EC 3.2.1.1) | protein | 496 | 29% helix, 24% strand | P04746 |
Ligands and binding sites
- B0D · (2R,3S,4R,5R,6R)-2,6-difluoro-2-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol · ligand · 2 copies · chains A
- B9D · 5-fluoro-alpha-L-idopyranose · ligand · chains A
- BGC · 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.57 | 0.78 | 23 | B9D, BGC |
| 2 | 80 | 0.38 | 0.78 | 18 | empty |
| 3 | 81 | 0.33 | 0.75 | 19 | empty |
Modifications
Observed in the structure: 5 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, cyclization).
Compared structures
- 3IJ9 · Directed 'in situ' Elongation as a Strategy to Characterize the Covalent Glycosyl-Enzyme… · 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 3IJ9 · PDBe 3IJ9 · UniProt P04746
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