Structure of PDB 7pod Chain A Binding Site BS01

Receptor Information
>7pod Chain A (length=273) Species: 171101 (Streptococcus pneumoniae R6) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAYYQVVPVTANVYDSDGEKLSYISQGSVVWLDKDRKSDDKRLAITISGL
SGYMKTEDLQALDASKDFIPYYESDGHRFYHYVAQNASIPVASHLSDMEV
GKKYYSADGLHFDGFKLENPFLFKDLTEATNYSAEELDKVFSLLNINNSL
LENKGATFKEAEEHYHINALYLLAHSALESNWGRSKIAKDKNNFFGITAY
DTTPYLSAKTFDDVDKGILGATKWIKENYIDRGRTFLGNKASGMNVEYAS
DPYWGEKIASVMMKINEKLGGKD
Ligand information
Ligand IDAMV
InChIInChI=1S/C12H21NO8/c1-5(11(17)18)20-10-8(13-6(2)15)12(19-3)21-7(4-14)9(10)16/h5,7-10,12,14,16H,4H2,1-3H3,(H,13,15)(H,17,18)/t5-,7-,8-,9-,10-,12-/m1/s1
InChIKeyUXEQYDNCHCKBIL-PKKPQKKZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C(=O)O)OC1C(C(OC(C1O)CO)OC)NC(=O)C
OpenEye OEToolkits 1.5.0C[C@H](C(=O)O)O[C@@H]1[C@H]([C@@H](O[C@@H]([C@H]1O)CO)OC)NC(=O)C
CACTVS 3.341CO[CH]1O[CH](CO)[CH](O)[CH](O[CH](C)C(O)=O)[CH]1NC(C)=O
ACDLabs 10.04O=C(O)C(OC1C(O)C(OC(OC)C1NC(=O)C)CO)C
CACTVS 3.341CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O[C@H](C)C(O)=O)[C@H]1NC(C)=O
FormulaC12 H21 N O8
Namemethyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside;
METHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE;
methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucoside;
methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-D-glucoside;
methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-glucoside
ChEMBL
DrugBank
ZINCZINC000058650293
PDB chain7pod Chain B 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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PDB7pod Molecular basis of the final step of cell division in Streptococcus pneumoniae.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		E585 D657
Binding residue
(residue number reindexed from 1)		E179 D251
Annotation score1
Enzymatic activity
Enzyme Commision number 3.2.1.96: mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase.
Gene Ontology
Molecular Function
GO:0004040 amidase activity

View graph for
Molecular Function
External links
PDB RCSB:7pod, PDBe:7pod, PDBj:7pod
PDBsum7pod
PubMed37418323
UniProtP59206|LYTB_STRR6 Putative endo-beta-N-acetylglucosaminidase (Gene Name=lytB)

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