› 1u2y

X-ray diffraction
1.95Å resolution

In situ extension as an approach for identifying novel alpha-amylase inhibitors, structure containing D-gluconhydroximo-1,5-lactam

Released:
DOI: 10.2210/pdb1u2y/pdb
PDB entry 1u2y coloured by chain, front view.
PDB entry 1u2y coloured by chain, side view.
PDB entry 1u2y coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
In situ extension as an approach for identifying novel alpha-amylase inhibitors.
Numao S, Damager I, Li C, Wrodnigg TM, Begum A, Overall CM, Brayer GD, Withers SG
J Biol Chem 279 48282-91 (2004)
PMID: 15304511

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138163 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pancreatic alpha-amylase Chain: A
Molecule details ›
Chain: A
Length: 496 amino acids
Theoretical weight: 55.93 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P04746 (Residues: 16-511; Coverage: 100%)
Gene name: AMY2A
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand NAG 1 x NAG
Ligand CA 1 x CA
Ligand CL 1 x CL
Ligand GOX 1 x GOX
1 modified residue:
Ligand PCA 1 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P212121
Unit cell:
a: 52.8Å b: 68.9Å c: 132.4Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.168 0.167 0.198
Expression system: Komagataella pastoris

Quick links

Citations

3 review citations

Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges.
Guedes et al. (2018)
2 more

2 mentions without citation

Crystallographic refinement of ligand complexes.
Kleywegt GJ. (2007)
1 more