Structure of PDB 7pod Chain A Binding Site BS02

Receptor Information

>7pod Chain A (length=273) Species: 171101 (Streptococcus pneumoniae R6)

AAYYQVVPVTANVYDSDGEKLSYISQGSVVWLDKDRKSDDKRLAITISGL
SGYMKTEDLQALDASKDFIPYYESDGHRFYHYVAQNASIPVASHLSDMEV
GKKYYSADGLHFDGFKLENPFLFKDLTEATNYSAEELDKVFSLLNINNSL
LENKGATFKEAEEHYHINALYLLAHSALESNWGRSKIAKDKNNFFGITAY
DTTPYLSAKTFDDVDKGILGATKWIKENYIDRGRTFLGNKASGMNVEYAS
DPYWGEKIASVMMKINEKLGGKD

Ligand information

• Ligand ID: AMU
• InChI: InChI=1S/C11H19NO8/c1-4(10(16)17)19-9-7(12-5(2)14)11(18)20-6(3-13)8(9)15/h4,6-9,11,13,15,18H,3H2,1-2H3,(H,12,14)(H,16,17)/t4-,6-,7-,8-,9-,11-/m1/s1
• InChIKey: MNLRQHMNZILYPY-YVNCZSHWSA-N
• SMILES:
  CACTVS 3.341: C[CH](O[CH]1[CH](O)[CH](CO)O[CH](O)[CH]1NC(C)=O)C(O)=O
  ACDLabs 10.04: O=C(O)C(OC1C(O)C(OC(O)C1NC(=O)C)CO)C
  OpenEye OEToolkits 1.5.0: CC(C(=O)O)OC1C(C(OC(C1O)CO)O)NC(=O)C
  CACTVS 3.341: C[C@@H](O[C@H]1[C@H](O)[C@@H](CO)O[C@@H](O)[C@@H]1NC(C)=O)C(O)=O
  OpenEye OEToolkits 1.5.0: C[C@H](C(=O)O)O[C@@H]1[C@H]([C@@H](O[C@@H]([C@H]1O)CO)O)NC(=O)C
• Formula: C11 H19 N O8
• Name: N-acetyl-beta-muramic acid;
  N-acetyl-muramic acid;
  BETA-N-ACETYLMURAMIC ACID
• ZINC: ZINC000004095908
• PDB chain: 7pod Chain B Residue 3

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7pod Molecular basis of the final step of cell division in Streptococcus pneumoniae.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): Y429 T604 Y606 D607 W630 Y635 E653 Y654
• Binding residue (residue number reindexed from 1): Y23 T198 Y200 D201 W224 Y229 E247 Y248
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.2.1.96: mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase.

Gene Ontology

Molecular Function

• GO:0004040 amidase activity

External links

• PDB: RCSB:7pod, PDBe:7pod, PDBj:7pod
• PDBsum: 7pod
• PubMed: 37418323
• UniProt: P59206|LYTB_STRR6 Putative endo-beta-N-acetylglucosaminidase (Gene Name=lytB)