Structure of PDB 4dki Chain A Binding Site BS02

Receptor Information
>4dki Chain A (length=641) Species: 93062 (Staphylococcus aureus subsp. aureus COL) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKDKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLG
VKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWK
LDWDHSVIIPGMQKDQSIHIENLKSERGKILDRNNVELANTGTAYEIGIV
PKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYL
SDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGYKD
DAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDI
QLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYG
MSNEEYNKLTEDKKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTS
YKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALEL
GSKKFEKGMKKLGVGEDIPSDYPFYNAQISNKNLDNEILLADSGYGQGEI
LINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDG
MQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQETGRQIGWFISYDKDNP
NMMMAINVKDVQDMASYNAKISGKVYDELYENGNKKYDIDE
Ligand information
Ligand IDBCT
InChIInChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-1
InChIKeyBVKZGUZCCUSVTD-UHFFFAOYSA-M
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(=O)(O)[O-]
CACTVS 3.341OC([O-])=O
ACDLabs 10.04[O-]C(=O)O
FormulaC H O3
NameBICARBONATE ION
ChEMBL
DrugBank
ZINC
PDB chain4dki Chain A Residue 703 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4dki Structural Insights into the Anti-methicillin-resistant Staphylococcus aureus (MRSA) Activity of Ceftobiprole.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		Q137 K138
Binding residue
(residue number reindexed from 1)		Q113 K114
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0008658 penicillin binding
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
GO:0071972 peptidoglycan L,D-transpeptidase activity
Biological Process
GO:0046677 response to antibiotic
GO:0071555 cell wall organization
Cellular Component
GO:0016020 membrane

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4dki, PDBe:4dki, PDBj:4dki
PDBsum4dki
PubMed22815485
UniProtA0A0H2WXF8

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