Structure of PDB 6mdv Chain A Binding Site BS02

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 3 [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]
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)		R72 W74 E288 E289 A291
Binding residue
(residue number reindexed from 1)		R27 W29 E243 E244 A246
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)

[Back to BioLiP]