Structure of PDB 5oyd Chain A Binding Site BS01

Receptor Information
>5oyd Chain A (length=370) Species: 498211 (Cellvibrio japonicus Ueda107) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLYPSYNTSPAAPDSTGMQSTAVQLAGKIRLGWNIGNTMEAIGGETAWGN
PMVSNELLKLVKDSGFDAVRIPVAWDQYANQESAEISAAWLNRVKQVVQM
AIDNELYVLINIHWDGGWLENNITPAKKDENNAKQKAFWEQIATHLRDFD
EHLLFAGTNEPNAENAEQMDVLNSYLQTFVDAVRSTGGKNAYRVLVLQGP
VTDIEKTNELWTHMPADTATDRLMAEVHFYTPYNFALMRQDESWGKQFYY
WGEGFLSTTDTERNPTWGEEATIDQLFDLMKTKFVDQGIPVVLGEFSAMR
RTNLTGDALTLHLAGRAYYHKYVTQQALARGLLPFYWDNGGNDNFSSGIF
NRQQNTVFDQQVLDALLEGA
Ligand information
Ligand IDNBG
InChIInChI=1S/C8H15NO6/c1-3(11)9-8-7(14)6(13)5(12)4(2-10)15-8/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6+,7-,8-/m1/s1
InChIKeyIBONACLSSOLHFU-JAJWTYFOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=O)N[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O)O)O
CACTVS 3.341CC(=O)N[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O
CACTVS 3.341CC(=O)N[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O
ACDLabs 10.04O=C(NC1OC(C(O)C(O)C1O)CO)C
OpenEye OEToolkits 1.5.0CC(=O)NC1C(C(C(C(O1)CO)O)O)O
FormulaC8 H15 N O6
NameN-acetyl-beta-D-glucopyranosylamine;
1-N-ACETYL-BETA-D-GLUCOSAMINE;
N-acetyl-beta-D-glucosylamine;
N-acetyl-D-glucosylamine;
N-acetyl-glucosylamine
ChEMBLCHEMBL335315
DrugBankDB02320
ZINC
PDB chain5oyd Chain C Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5oyd In vitro and in vivo characterization of threeCellvibrio japonicusglycoside hydrolase family 5 members reveals potent xyloglucan backbone-cleaving functions.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		H208 N254 E255 H323 Y325 E390 W432
Binding residue
(residue number reindexed from 1)		H113 N159 E160 H228 Y230 E295 W337
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=2.75,Kd=1.78mM
Enzymatic activity
Enzyme Commision number 3.2.1.4: cellulase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
Biological Process
GO:0000272 polysaccharide catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5oyd, PDBe:5oyd, PDBj:5oyd
PDBsum5oyd
PubMed29467823
UniProtB3PD52

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