Structure of PDB 1kcd Chain A Binding Site BS01

Receptor Information
>1kcd Chain A (length=333) Species: 58369 (Chondrostereum purpureum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CTVKSVDDAKDIAGCSAVTLNGFTVPAGNTLVLNPDKGATVTMAGDITFA
KTTLDGPLFTIDGTGINFVGADHIFDGNGALYWDGKGTNNGTHKPHPFLK
IKGSGTYKKFEVLNSPAQAISVGPTDAHLTLDGITVDDFAGDTKNLGHNT
DGFDVSANNVTIQNCIVKNQDDCIAINDGNNIRFENNQCSGGHGISIGSI
ATGKHVSNVVIKGNTVTRSMYGVRIKAQRTATSASVSGVTYDANTISGIA
KYGVLISQSYPDDVGNPGTGAPFSDVNFTGGATTIKVNNAATRVTVECGN
CSGNWNWSQLTVTGGKAGTIKSDKAKITGGQYL
Ligand information
Ligand IDGTK
InChIInChI=1S/C6H10O7/c7-1-2(8)6(12)13-4(1)3(9)5(10)11/h1-4,6-9,12H,(H,10,11)/t1-,2-,3+,4-,6-/m1/s1
InChIKeyOEVWLAOZEALENB-ORELYVPDSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)C(O)C1OC(O)C(O)C1O
OpenEye OEToolkits 1.7.2[C@H]1([C@H]([C@@H](O[C@H]1[C@@H](C(=O)O)O)O)O)O
CACTVS 3.370O[CH]1O[CH]([CH](O)[CH]1O)[CH](O)C(O)=O
CACTVS 3.370O[C@@H]1O[C@H]([C@H](O)[C@H]1O)[C@H](O)C(O)=O
OpenEye OEToolkits 1.7.2C1(C(C(OC1C(C(=O)O)O)O)O)O
FormulaC6 H10 O7
Namebeta-D-galactofuranuronic acid;
beta-D-galacturonic acid;
D-galacturonic acid;
galacturonic acid
ChEMBL
DrugBank
ZINC
PDB chain1kcd Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1kcd Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.
Resolution1.15 Å
Binding residue
(original residue number in PDB)		Q120 N151 D153 D173 S201 K228 Y262
Binding residue
(residue number reindexed from 1)		Q118 N149 D151 D171 S199 K226 Y260
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D153 D173 D174 H195 R226 K228
Catalytic site (residue number reindexed from 1) D151 D171 D172 H193 R224 K226
Enzyme Commision number 3.2.1.15: endo-polygalacturonase.
Gene Ontology
Molecular Function
GO:0004650 polygalacturonase activity
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1kcd, PDBe:1kcd, PDBj:1kcd
PDBsum1kcd
PubMed12022868
UniProtP79074

[Back to BioLiP]