Structure of PDB 2ex8 Chain A Binding Site BS01

Receptor Information
>2ex8 Chain A (length=456) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NVDEYITQLPAGANLALMVQKVGASAPAIDYHSQQMALPASTQKVITALA
ALIQLGPDFRFTTTLETKGNVENGVLKGDLVARFGADPTLKRQDIRNMVA
TLKKSGVNQIDGNVLIDTSIFASHDKAPGWPWNDMTQCFSAPPAAAIVDR
NCFSVSLYSAPKPGDMAFIRVASYYPVTMFSQVRTLPRGSAEAQYCELDV
VPGDLNRFTLTGCLPQRSEPLPLAFAVQDGASYAGAILKYELKQAGITWS
GTLLRQTQVNEPGTVVASKQSAPLHDLLKIMLKKSDNMIADTVFRMIGHA
RFNVPGTWRAGSDAVRQILRQQAGVDIGNTIIADGSGLSRHNLIAPATMM
QVLQYIAQHDNELNFISMLPLAGYDGSLQYRAGLHQAGVDGKVSAKTGSL
QGVYNLAGFITTASGQRMAFVQYLSGYAVEPADQRNRRIPLVRFESRLYK
DIYQNN
Ligand information
Ligand IDPNM
InChIInChI=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
InChIKeyOGFZUTGOGYUTKZ-KWCYVHTRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1(C(NC(S1)C(C=O)NC(=O)Cc2ccccc2)C(=O)O)C
OpenEye OEToolkits 1.5.0CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)Cc2ccccc2)C(=O)O)C
ACDLabs 10.04O=C(NC(C=O)C1SC(C(N1)C(=O)O)(C)C)Cc2ccccc2
CACTVS 3.341CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)Cc2ccccc2)C=O
CACTVS 3.341CC1(C)S[CH](N[CH]1C(O)=O)[CH](NC(=O)Cc2ccccc2)C=O
FormulaC16 H20 N2 O4 S
NameOPEN FORM - PENICILLIN G
ChEMBL
DrugBank
ZINCZINC000006591277
PDB chain2ex8 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ex8 Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics
Resolution1.6 Å
Binding residue
(original residue number in PDB)		S62 F160 S306 N308 L359 T418 G419 S420
Binding residue
(residue number reindexed from 1)		S41 F139 S285 N287 L338 T397 G398 S399
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
3.4.21.-
Gene Ontology
Molecular Function
GO:0004175 endopeptidase activity
GO:0004180 carboxypeptidase activity
GO:0004185 serine-type carboxypeptidase activity
GO:0004252 serine-type endopeptidase activity
GO:0005515 protein binding
GO:0008658 penicillin binding
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
GO:0016787 hydrolase activity
Biological Process
GO:0000270 peptidoglycan metabolic process
GO:0006508 proteolysis
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0043093 FtsZ-dependent cytokinesis
GO:0046677 response to antibiotic
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005886 plasma membrane
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2ex8, PDBe:2ex8, PDBj:2ex8
PDBsum2ex8
PubMed16411754
UniProtP24228|DACB_ECOLI D-alanyl-D-alanine carboxypeptidase DacB (Gene Name=dacB)

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