Structure of PDB 5oyd Chain B Binding Site BS01

Receptor Information

>5oyd Chain B (length=371) Species: 498211 (Cellvibrio japonicus Ueda107)

GLYPSYNTSPAAPDSTGMQSTAVQLAGKIRLGWNIGNTMEAIGGETAWGN
PMVSNELLKLVKDSGFDAVRIPVAWDQYANQESAEISAAWLNRVKQVVQM
AIDNELYVLINIHWDGGWLENNITPAKKDENNAKQKAFWEQIATHLRDFD
EHLLFAGTNEPNAENAEQMDVLNSYLQTFVDAVRSTGGKNAYRVLVLQGP
VTDIEKTNELWTHMPADTATDRLMAEVHFYTPYNFALMRQDESWGKQFYY
WGEGFLSTTDTERNPTWGEEATIDQLFDLMKTKFVDQGIPVVLGEFSAMR
RTNLTGDALTLHLAGRAYYHKYVTQQALARGLLPFYWDNGGNDNFSSGIF
NRQQNTVFDQQVLDALLEGAG

Ligand information

• Ligand ID: NBG
• InChI: InChI=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
• InChIKey: IBONACLSSOLHFU-JAJWTYFOSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(=O)N[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O)O)O
  CACTVS 3.341: CC(=O)N[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: CC(=O)N[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O
  ACDLabs 10.04: O=C(NC1OC(C(O)C(O)C1O)CO)C
  OpenEye OEToolkits 1.5.0: CC(=O)NC1C(C(C(C(O1)CO)O)O)O
• Formula: C8 H15 N O6
• Name: N-acetyl-beta-D-glucopyranosylamine;
  1-N-ACETYL-BETA-D-GLUCOSAMINE;
  N-acetyl-beta-D-glucosylamine;
  N-acetyl-D-glucosylamine;
  N-acetyl-glucosylamine
• ChEMBL: CHEMBL335315
• DrugBank: DB02320
• PDB chain: 5oyd Chain D Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5oyd In vitro and in vivo characterization of threeCellvibrio japonicusglycoside hydrolase family 5 members reveals potent xyloglucan backbone-cleaving functions.
• Resolution: 2.1 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 score: 1

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

External links

• PDB: RCSB:5oyd, PDBe:5oyd, PDBj:5oyd
• PDBsum: 5oyd
• PubMed: 29467823
• UniProt: B3PD52