Structure of PDB 3bec Chain A Binding Site BS01

Receptor Information
>3bec Chain A (length=352) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NIKTMIPGVPQIDAESYILIDYNSGKVLAEQNADVRRDPASLTKMMTSYV
IGQAMKAGKFKETDLVTIGNDAWATGNPVFKGSSLMFLKPGMQVPVSQLI
RGINLQSGNDACVAMADFAAGSQDAFVGLMNSYVNALGLKNTHFQTVHGL
DADGQYSSARDMALIGQALIRDVPNEYSIYKEKEFTFNGIRQLNRNGLLW
DNSLNVDGIKTGHTDKAGYNLVASATEGQMRLISAVMGGRTFKGREAESK
KLLTWGFRFFETVNPLKVGKEFASEPVWFGDSDRASLGVDKDVYLTIPRG
RMKDLKASYVLNSSELHAPLQKNQVVGTINFQLDGKTIEQRPLVVLQEIP
EG
Ligand information
Ligand IDHJ2
InChIInChI=1S/C15H23N3O7S/c1-7-6-26-12(18-10(7)14(22)23)11(15(24)25)17-9(19)5-3-2-4-8(16)13(20)21/h8,11-12,18H,2-6,16H2,1H3,(H,17,19)(H,20,21)(H,22,23)(H,24,25)/t8-,11-,12+/m0/s1
InChIKeyHJUSKFHSSKMVMT-KPXOXKRLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=C(N[C@H](SC1)[C@@H](C(=O)O)NC(=O)CCCC[C@@H](C(=O)O)N)C(=O)O
OpenEye OEToolkits 1.5.0CC1=C(NC(SC1)C(C(=O)O)NC(=O)CCCCC(C(=O)O)N)C(=O)O
CACTVS 3.341CC1=C(N[CH](SC1)[CH](NC(=O)CCCC[CH](N)C(O)=O)C(O)=O)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCCC(=O)NC(C(=O)O)C1SCC(=C(N1)C(=O)O)C
CACTVS 3.341CC1=C(N[C@H](SC1)[C@H](NC(=O)CCCC[C@H](N)C(O)=O)C(O)=O)C(O)=O
FormulaC15 H23 N3 O7 S
Name(2R)-2-[(R)-{[(6S)-6-amino-6-carboxyhexanoyl]amino}(carboxy)methyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000103544768
PDB chain3bec Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3bec Crystal structures of complexes of bacterial DD-peptidases with peptidoglycan-mimetic ligands: the substrate specificity puzzle
Resolution1.6 Å
Binding residue
(original residue number in PDB)		S44 R198 T214 G215 H216 R248
Binding residue
(residue number reindexed from 1)		S41 R195 T211 G212 H213 R245
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
3.5.2.6: beta-lactamase.
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008658 penicillin binding
GO:0008800 beta-lactamase activity
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
GO:0042803 protein homodimerization activity
Biological Process
GO:0000270 peptidoglycan metabolic process
GO:0006508 proteolysis
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005886 plasma membrane
GO:0030288 outer membrane-bounded periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3bec, PDBe:3bec, PDBj:3bec
PDBsum3bec
PubMed18602645
UniProtP0AEB2|DACA_ECOLI D-alanyl-D-alanine carboxypeptidase DacA (Gene Name=dacA)

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