Structure of PDB 6mdv Chain B Binding Site BS01

Receptor Information
>6mdv Chain B (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 IDBMA
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-RWOPYEJCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
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
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
Namebeta-D-mannopyranose;
beta-D-mannose;
D-mannose;
mannose
ChEMBL
DrugBank
ZINCZINC000003830679
PDB chain6mdv Chain D Residue 2 [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)		D108 E288 Y339
Binding residue
(residue number reindexed from 1)		D63 E243 Y294
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

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Molecular Function
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Biological Process
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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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