Structure of PDB 6yq9 Chain AAA Binding Site BS01

Receptor Information

>6yq9 Chain AAA (length=476) Species: 5062 (Aspergillus oryzae)

ATPADWRSQSIYFLLTDRFARTDGSTTATCNTADQKYCGGTWQGIIDKLD
YIQGMGFTAIWITPVTAQLPQTTAYGDAYHGYWQQDIYSLNENYGTADDL
KALSSALHERGMYLMVDVVANHMGYDGAGSSVDYSVFKPFSSQDYFHPFC
FIQNYEDQTQVEDCWLGDNTVSLPDLDTTKDVVKNEWYDWVGSLVSNYSI
DGLRIDTVKHVQKDFWPGYNKAAGVYCIGEVLDGDPAYTCPYQNVMDGVL
NYPIYYPLLNAFKSTSGSMDDLYNMINTVKSDCPDSTLLGTFVENHDNPR
FASYTNDIALAKNVAAFIILNDGIPIIYAGQEQHYAGGNDPANREATWLS
GYPTDSELYKLIASANAIRNYAISKDTGFVTYKNWPIYKDDTTIAMRKGT
DGSQIVTILSNKGASGDSYTLSLSGAGYTAGQQLTEVIGCTTVTVGSDGN
VPVPMAGGLPRVLYPTEKLAGSKICS

Ligand information

• Ligand ID: 5QP
• InChI: InChI=1S/C13H24O10/c14-2-4-5(16)1-6(17)8(18)12(4)23-13-11(21)10(20)9(19)7(3-15)22-13/h4-21H,1-3H2/t4-,5+,6-,7+,8+,9+,10-,11+,12+,13+/m0/s1
• InChIKey: POWCVSWKDOOEBI-FELRGSJNSA-N
• SMILES:
  OpenEye OEToolkits 2.0.4: C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1O)O)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)CO)O
  CACTVS 3.385: OC[CH]1O[CH](O[CH]2[CH](O)[CH](O)C[CH](O)[CH]2CO)[CH](O)[CH](O)[CH]1O
  CACTVS 3.385: OC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)C[C@@H](O)[C@@H]2CO)[C@H](O)[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 2.0.4: C1C(C(C(C(C1O)O)OC2C(C(C(C(O2)CO)O)O)O)CO)O
• Formula: C13 H24 O10
• Name: (1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl alpha-D-glucopyranoside;
  (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(1~{R},2~{S},3~{R},5~{S},6~{R})-2-(hydroxymethyl)-3,5,6-tris(oxida nyl)cyclohexyl]oxy-oxane-3,4,5-triol;
  gluosyl epi-cyclophellitol (bound form);
  (1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl alpha-D-glucoside;
  (1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl D-glucoside;
  (1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl glucoside
• ZINC: ZINC000584905298
• PDB chain: 6yq9 Chain AAA Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6yq9 Activity-Based Protein Profiling of Retaining alpha-Amylases in Complex Biological Samples.
• Resolution: 1.55 Å
• Binding residue (original residue number in PDB): H80 Y82 W83 H122 R204 D206 T207 H296 D297 D340 R344
• Binding residue (residue number reindexed from 1): H80 Y82 W83 H122 R204 D206 T207 H296 D297 D340 R344
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): R204 D206 E230 H296 D297
• Catalytic site (residue number reindexed from 1): R204 D206 E230 H296 D297
• Enzyme Commision number: 3.2.1.1: alpha-amylase.

Gene Ontology

Molecular Function

• GO:0004556 alpha-amylase activity
• GO:0005509 calcium ion binding
• GO:0043169 cation binding

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0016052 carbohydrate catabolic process

External links

• PDB: RCSB:6yq9, PDBe:6yq9, PDBj:6yq9
• PDBsum: 6yq9
• PubMed: 33497208
• UniProt: A0A1S9DH83