Structure of PDB 3mze Chain A Binding Site BS01

Receptor Information
>3mze 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 ID1QL
InChIInChI=1S/C16H19N3O7S2/c1-25-16(8-20,19-11(21)5-10-3-2-4-27-10)14-18-12(13(22)23)9(7-28-14)6-26-15(17)24/h2-4,8,14,18H,5-7H2,1H3,(H2,17,24)(H,19,21)(H,22,23)/t14-,16+/m1/s1
InChIKeyIYZWSAWEHPQLHS-ZBFHGGJFSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CO[C](NC(=O)Cc1sccc1)(C=O)[CH]2NC(=C(COC(N)=O)CS2)C(O)=O
OpenEye OEToolkits 1.7.6COC(C=O)(C1NC(=C(CS1)COC(=O)N)C(=O)O)NC(=O)Cc2cccs2
CACTVS 3.370CO[C@@](NC(=O)Cc1sccc1)(C=O)[C@@H]2NC(=C(COC(N)=O)CS2)C(O)=O
ACDLabs 12.01O=CC(OC)(NC(=O)Cc1sccc1)C2SCC(=C(N2)C(=O)O)COC(=O)N
OpenEye OEToolkits 1.7.6CO[C@@](C=O)([C@@H]1NC(=C(CS1)COC(=O)N)C(=O)O)NC(=O)Cc2cccs2
FormulaC16 H19 N3 O7 S2
Name(2R)-5-[(carbamoyloxy)methyl]-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid;
Cefoxitin, bound form
ChEMBL
DrugBank
ZINC
PDB chain3mze Chain A Residue 364 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3mze Crystal structures of covalent complexes of beta-lactam antibiotics with Escherichia coli penicillin-binding protein 5: toward an understanding of antibiotic specificity
Resolution2.1 Å
Binding residue
(original residue number in PDB)
S44 G85 S86 S87 N112 L153 T214 G215 H216 T217 F245 R248
Binding residue
(residue number reindexed from 1)
S41 G82 S83 S84 N109 L150 T211 G212 H213 T214 F242 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:3mze, PDBe:3mze, PDBj:3mze
PDBsum3mze
PubMed20726582
UniProtP0AEB2|DACA_ECOLI D-alanyl-D-alanine carboxypeptidase DacA (Gene Name=dacA)

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