Structure of PDB 3dyb Chain A Binding Site BS01

Receptor Information

>3dyb Chain A (length=279) Species: 37998 (Parengyodontium album)

AAQTNAPWGLARISSTSPGTSTYYYDESAGQGSCVYVIDTGIEASHPEFE
GRAQMVKTYYYSSRDGNGHGTHCAGTVGSRTYGVAKKTQLFGVKVLDDNG
SGQYSTIIAGMDFVASDKNNRNCPKGVVASLSLGGGYSSSVNSAAARLQS
SGVMVAVAAGNNNADARNYSPASEPSVCTVGASDRYDRRSSFSNYGSVLD
IFGPGTDILSTWIGGSTRSISGTSMATPHVAGLAAYLMTLGKTTAASACR
YIADTANKGDLSNIPFGTVNLLAYNNYQA

Ligand information

• Ligand ID: ADA
• InChI: InChI=1S/C6H10O7/c7-1-2(8)4(5(10)11)13-6(12)3(1)9/h1-4,6-9,12H,(H,10,11)/t1-,2+,3+,4-,6-/m0/s1
• InChIKey: AEMOLEFTQBMNLQ-BKBMJHBISA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1(C(C(OC(C1O)O)C(=O)O)O)O
  CACTVS 3.341: O[CH]1O[CH]([CH](O)[CH](O)[CH]1O)C(O)=O
  CACTVS 3.341: O[C@H]1O[C@@H]([C@H](O)[C@H](O)[C@H]1O)C(O)=O
  ACDLabs 10.04: O=C(O)C1OC(O)C(O)C(O)C1O
  OpenEye OEToolkits 1.5.0: [C@@H]1([C@H]([C@H](O[C@@H]([C@@H]1O)O)C(=O)O)O)O
• Formula: C6 H10 O7
• Name: alpha-D-galactopyranuronic acid;
  alpha-D-galacturonic acid;
  D-galacturonic acid;
  galacturonic acid;
  ALPHA D-GALACTURONIC ACID
• DrugBank: DB03511
• ZINC: ZINC000004228259
• PDB chain: 3dyb Chain B Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3dyb High-resolution structure of proteinase K cocrystallized with digalacturonic acid.
• Resolution: 1.32 Å
• Binding residue (original residue number in PDB): S143 A146 R147 S150
• Binding residue (residue number reindexed from 1): S143 A146 R147 S150
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): D39 H69 N161 S224
• Catalytic site (residue number reindexed from 1): D39 H69 N161 S224
• Enzyme Commision number: 3.4.21.64: peptidase K.

Gene Ontology

Molecular Function

• GO:0004252 serine-type endopeptidase activity
• GO:0008236 serine-type peptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:3dyb, PDBe:3dyb, PDBj:3dyb
• PDBsum: 3dyb
• PubMed: 19255463
• UniProt: P06873|PRTK_PARAQ Proteinase K (Gene Name=PROK)