Structure of PDB 3mzf Chain A Binding Site BS01

Receptor Information
>3mzf Chain A (length=355) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LNIKTMIPGVPQIDAESYILIDYNSGKVLAEQNADVRRDPASLTKMMTSY
VIGQAMKAGKFKETDLVTIGNDAWATGNPVFKGSSLMFLKPGMQVPVSQL
IRGINLQSGNDACVAMADFAAGSQDAFVGLMNSYVNALGLKNTHFQTVHG
LDADGQYSSARDMALIGQALIRDVPNEYSIYKEKEFTFNGIRQLNRNGLL
WDNSLNVDGIKTGHTDKAGYNLVASATEGQMRLISAVMGGRTFKGREAES
KKLLTWGFRFFETVNPLKVGKEFASEPVWFGDSDRASLGVDKDVYLTIPR
GRMKDLKASYVLNSSELHAPLQKNQVVGTINFQLDGKTIEQRPLVVLQEI
PEGNF
Ligand information
Ligand IDIM2
InChIInChI=1S/C12H19N3O4S/c1-7(17)8(5-16)9-4-10(11(15-9)12(18)19)20-3-2-14-6-13/h5-9,15,17H,2-4H2,1H3,(H2,13,14)(H,18,19)/t7-,8-,9-/m1/s1
InChIKeyUACUABDJLSUFFC-IWSPIJDZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6[H]/N=C/NCCSC1=C(N[C@H](C1)[C@H](C=O)[C@@H](C)O)C(=O)O
ACDLabs 12.01O=C(O)C1=C(SCCNC=[N@H])CC(N1)C(C=O)C(O)C
CACTVS 3.370C[C@@H](O)[C@@H](C=O)[C@H]1CC(=C(N1)C(O)=O)SCCNC=N
OpenEye OEToolkits 1.7.6CC(C(C=O)C1CC(=C(N1)C(=O)O)SCCNC=N)O
CACTVS 3.370C[CH](O)[CH](C=O)[CH]1CC(=C(N1)C(O)=O)SCCNC=N
FormulaC12 H19 N3 O4 S
Name(5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid;
IMIPENEM, open form;
N-FORMIMIDOYL-THIENAMYCINE, open form
ChEMBL
DrugBank
ZINCZINC000103040234
PDB chain3mzf Chain A Residue 364 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3mzf Crystal structures of covalent complexes of beta-lactam antibiotics with Escherichia coli penicillin-binding protein 5: toward an understanding of antibiotic specificity
Resolution1.5 Å
Binding residue
(original residue number in PDB)
S44 G85 S86 N112 T214 G215 H216
Binding residue
(residue number reindexed from 1)
S42 G83 S84 N110 T212 G213 H214
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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Biological Process

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Cellular Component
External links
PDB RCSB:3mzf, PDBe:3mzf, PDBj:3mzf
PDBsum3mzf
PubMed20726582
UniProtP0AEB2|DACA_ECOLI D-alanyl-D-alanine carboxypeptidase DacA (Gene Name=dacA)

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