Structure of PDB 5zqd Chain D Binding Site BS01

Receptor Information

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

QPNLYLSANAAAVYSVENGEALYEQNADKVMPIASLSKLMTAFLVLEAVD
NNELSWDEKLDLVRLDDPSAVSLYAITQKRTWSVRDLYSAMLTMSANDAA
ETLGDRLDGADFPKEMNNQAKKLGMSSKTTFVSASGLDVDGKSAVSTTKD
LFLLSSKLISTHPEVLETTSKPTVTTDKGAKLESTNDLLGSIQGLDGLKT
GFTDEAGYCFIGTAERGGKRVISIVLDAGTAEKRFKDTEKLMEVGFK

Ligand information

• Ligand ID: CEF
• InChI: InChI=1S/C14H15N5O5S2/c1-6-4-25-12(18-9(6)13(22)23)7(3-20)16-11(21)10(19-24-2)8-5-26-14(15)17-8/h3,5,7,12H,1,4H2,2H3,(H2,15,17)(H,16,21)(H,22,23)/b19-10-/t7-,12-/m1/s1
• InChIKey: NRYMPLKBKFIWQC-YVCCLBOHSA-N
• SMILES:
  CACTVS 3.385: CO\N=C(/C(=O)N[C@H](C=O)[C@H]1SCC(=C)C(=N1)C(O)=O)c2csc(N)n2
  OpenEye OEToolkits 1.7.6: CO/N=C(/c1csc(n1)N)\C(=O)NC(C=O)C2N=C(C(=C)CS2)C(=O)O
  OpenEye OEToolkits 1.7.6: CON=C(c1csc(n1)N)C(=O)NC(C=O)C2N=C(C(=C)CS2)C(=O)O
  CACTVS 3.385: CON=C(C(=O)N[CH](C=O)[CH]1SCC(=C)C(=N1)C(O)=O)c2csc(N)n2
• Formula: C14 H15 N5 O5 S2
• Name: CEFOTAXIME, C3' cleaved, open, bound form
• DrugBank: DB08375
• ZINC: ZINC000015605562
• PDB chain: 5zqd Chain D Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5zqd Crystal Structures of Penicillin-Binding Protein D2 from Listeria monocytogenes and Structural Basis for Antibiotic Specificity
• Resolution: 1.888 Å
• Binding residue (original residue number in PDB): S58 V94 S118 T223 G224 F225 T226 R257
• Binding residue (residue number reindexed from 1): S35 V71 S95 T200 G201 F202 T203 R234
• 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:5zqd, PDBe:5zqd, PDBj:5zqd
• PDBsum: 5zqd
• PubMed: 30082290
• UniProt: Q8Y3M3