Structure of PDB 6mdv Chain A Binding Site BS04

Receptor Information
>6mdv Chain A (length=787) Species: 1314 (Streptococcus pyogenes) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDQQVGAKLVQEIREGKRGPLYAGYFRTWHDRASTGIDGKQQHPENTMAE
VPKEVDILFVFHDHTASDSPFWSELKDSYVHKLHQQGTALVQTIGVNELN
GRTGLSKDYPDTPEGNKALAAAIVKAFVTDRGVDGLDIDIEHEFTNKRTP
EEDARALNVFKEIAQLIGKNGSDKSKLLIMDTTLSVENNPIFKGIAEDLD
YLLRQYYGSQGGEAEVDTINSDWNQYQNYIDASQFMIGFSFFEESASKGN
LWFDVNEYDPNNPEKGKDIEGTRAKKYAEWQPSTGGLKAGIFSYAIDRDG
VAHVPSTYKNRTSTNLQRHEVDNISHTDYTVSRKLKTLMTEDKRYDVIDQ
KDIPDPALREQIIQQVGQYKGDLERYNKTLVLTGDKIQNLKGLEKLSKLQ
KLELRQLSNVKEITPELLPESMKKDAELVMVGMTGLEKLNLSGLNRQTLD
GIDVNSITHLTSFDISHNSLDLSEKSEDRKLLMTLMEQVSNHQKITVKNT
AFENQKPKGYYPQTYDTKEGHYDVDNAEHDILTDFVFGTVTKRNTFIGDE
EAFAIYKEGAVDGRQYVSKDYTYEAFRKDYKGYKVHLTASNLGETVTSKV
TATTDETYLVDVSDGEKVVHHMKLNIGSGAIMMENLAKGAKVIGTSGDFE
QAKKIFDGEKSDRFFTWGQTNWIAFDLGEINLAKEWRLFNAETNTEIKTD
SSLNVAKGRLQILKDTTIDLEKMDIKNRKEYLSNDENWTDVAQMDDAKAI
FNSKLSNVLSRYWRFCVDGGASSYYPQYTELQILGQR
Ligand information
Ligand IDMAN
InChIInChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5+,6+/m1/s1
InChIKeyWQZGKKKJIJFFOK-PQMKYFCFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(O1)O)O)O)O)O
CACTVS 3.341OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O)O
ACDLabs 10.04OC1C(O)C(OC(O)C1O)CO
FormulaC6 H12 O6
Namealpha-D-mannopyranose;
alpha-D-mannose;
D-mannose;
mannose
ChEMBLCHEMBL365590
DrugBank
ZINCZINC000003860903
PDB chain6mdv Chain C Residue 7 [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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PDB6mdv Molecular Basis of Broad SpectrumN-Glycan Specificity and Processing of Therapeutic IgG Monoclonal Antibodies by Endoglycosidase S2.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		N142 E186 E188
Binding residue
(residue number reindexed from 1)		N97 E141 E143
Annotation score1
Enzymatic activity
Enzyme Commision number 3.2.1.96: mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0005509 calcium ion binding
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0033925 mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0042783 evasion of host immune response
Cellular Component
GO:0005576 extracellular region
GO:0043655 host extracellular space

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6mdv, PDBe:6mdv, PDBj:6mdv
PDBsum6mdv
PubMed30937380
UniProtT1WGN1|ENDS2_STRP9 Endo-beta-N-acetylglucosaminidase EndoS2 (Gene Name=endoS2)

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