Structure of PDB 6p54 Chain B Binding Site BS01

Receptor Information
>6p54 Chain B (length=326) Species: 485 (Neisseria gonorrhoeae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GALSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALANTPGR
NRAVTDMIEPGSAIKPFVIAKALDAGKTDLNERLNTQPYKIGPSPVRDTH
VYPSLDVRGIMQKSSNVGTSKLSARFGAEEMYDFYHELGIGVRMHSGFPG
ETAGLLRNWRRWRPIEQATMSFGYGLQLSLLQLARAYTALTHDGVLLPLS
FEKQAVAPQGKRIFKESTAREVRNLMVSVTEPGGTGTAGAVDGFDVGAKT
GTARKFVNGRYADNKHVATFIGFAPAKNPRVIVAVTIDEPTAHGYYGGVV
AGPPFKKIMGGSLNILGISPTKPLTA
Ligand information
Ligand IDCEF
InChIInChI=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
InChIKeyNRYMPLKBKFIWQC-YVCCLBOHSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CO\N=C(/C(=O)N[C@H](C=O)[C@H]1SCC(=C)C(=N1)C(O)=O)c2csc(N)n2
OpenEye OEToolkits 1.7.6CO/N=C(/c1csc(n1)N)\C(=O)NC(C=O)C2N=C(C(=C)CS2)C(=O)O
OpenEye OEToolkits 1.7.6CON=C(c1csc(n1)N)C(=O)NC(C=O)C2N=C(C(=C)CS2)C(=O)O
CACTVS 3.385CON=C(C(=O)N[CH](C=O)[CH]1SCC(=C)C(=N1)C(O)=O)c2csc(N)n2
FormulaC14 H15 N5 O5 S2
NameCEFOTAXIME, C3' cleaved, open, bound form
ChEMBL
DrugBankDB08375
ZINCZINC000015605562
PDB chain6p54 Chain B Residue 601 [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]
PDB6p54 Recognition of the beta-lactam carboxylate triggers acylation ofNeisseria gonorrhoeaepenicillin-binding protein 2.
Resolution1.83 Å
Binding residue
(original residue number in PDB)		S310 S362 N364 F420 G421 Y422 T498 G499 T500 A501 R502 Y544
Binding residue
(residue number reindexed from 1)		S62 S114 N116 F172 G173 Y174 T250 G251 T252 A253 R254 Y296
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
Gene Ontology
Molecular Function
GO:0008658 penicillin binding

View graph for
Molecular Function
External links
PDB RCSB:6p54, PDBe:6p54, PDBj:6p54
PDBsum6p54
PubMed31362987
UniProtP08149|PBP2_NEIGO Probable peptidoglycan D,D-transpeptidase PenA (Gene Name=penA)

[Back to BioLiP]