Structure of PDB 5zqb Chain A Binding Site BS01

Receptor Information

>5zqb Chain A (length=247) Species: 169963 (Listeria monocytogenes EGD-e)

QPNLYLSANAAAVYSVENGEALYEQNADKVMPIASLSKLMTAFLVLEAVD
NNELSWDEKLDLVRLDDPSAVSLYAITQKRTWSVRDLYSAMLTMSANDAA
ETLGDRLDGADFPKEMNNQAKKLGMSSKTTFVSASGLDVDGKSAVSTTKD
LFLLSSKLISTHPEVLETTSKPTVTTDKGAKLESTNDLLGSIQGLDGLKT
GFTDEAGYCFIGTAERGGKRVISIVLDAGTAEKRFKDTEKLMEVGFK

Ligand information

• Ligand ID: PNM
• InChI: InChI=1S/C16H20N2O4S/c1-16(2)13(15(21)22)18-14(23-16)11(9-19)17-12(20)8-10-6-4-3-5-7-10/h3-7,9,11,13-14,18H,8H2,1-2H3,(H,17,20)(H,21,22)/t11-,13+,14-/m1/s1
• InChIKey: OGFZUTGOGYUTKZ-KWCYVHTRSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1(C(NC(S1)C(C=O)NC(=O)Cc2ccccc2)C(=O)O)C
  OpenEye OEToolkits 1.5.0: CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)Cc2ccccc2)C(=O)O)C
  ACDLabs 10.04: O=C(NC(C=O)C1SC(C(N1)C(=O)O)(C)C)Cc2ccccc2
  CACTVS 3.341: CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)Cc2ccccc2)C=O
  CACTVS 3.341: CC1(C)S[CH](N[CH]1C(O)=O)[CH](NC(=O)Cc2ccccc2)C=O
• Formula: C16 H20 N2 O4 S
• Name: OPEN FORM - PENICILLIN G
• ZINC: ZINC000006591277
• PDB chain: 5zqb Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5zqb Crystal Structures of Penicillin-Binding Protein D2 from Listeria monocytogenes and Structural Basis for Antibiotic Specificity
• Resolution: 1.896 Å
• Binding residue (original residue number in PDB): S58 S92 A93 V94 S118 T223 G224 F225
• Binding residue (residue number reindexed from 1): S35 S69 A70 V71 S95 T200 G201 F202
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:5zqb, PDBe:5zqb, PDBj:5zqb
• PDBsum: 5zqb
• PubMed: 30082290
• UniProt: Q8Y3M3