Structure of PDB 3zvt Chain D Binding Site BS01

Receptor Information
>3zvt Chain D (length=466) Species: 72570 (Actinomadura sp. R39) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASN
MKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSA
EDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQ
ISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTG
AAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFE
EALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNN
GHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLS
RGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRG
TAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQD
AIAVRLAEYAGHQAPE
Ligand information
Ligand IDB07
InChIInChI=1S/C10H14BNO5/c1-16-7-4-3-5-8(17-2)9(7)10(13)12-6-11(14)15/h3-5,14-15H,6H2,1-2H3,(H,12,13)
InChIKeySXURQNHWSSEFLG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(c1c(OC)cccc1OC)NCB(O)O
CACTVS 3.385COc1cccc(OC)c1C(=O)NCB(O)O
OpenEye OEToolkits 1.9.2B(CNC(=O)c1c(cccc1OC)OC)(O)O
FormulaC10 H14 B N O5
Name2,6 DIMETHOXYBENZAMIDOBORONIC ACID
ChEMBLCHEMBL2035284
DrugBank
ZINC
PDB chain3zvt Chain D Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3zvt Unexpected Tricovalent Binding Mode of Boronic Acids within the Active Site of a Penicillin- Binding Protein.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		S49 K52 Y147 S298 K410
Binding residue
(residue number reindexed from 1)		S49 K52 Y147 S298 K410
Annotation score1
Binding affinityBindingDB: IC50=1300nM,Ki=1500nM
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:0004185 serine-type carboxypeptidase activity
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
Biological Process
GO:0000270 peptidoglycan metabolic process
GO:0006508 proteolysis
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0046677 response to antibiotic
GO:0071555 cell wall organization
Cellular Component
GO:0005576 extracellular region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3zvt, PDBe:3zvt, PDBj:3zvt
PDBsum3zvt
PubMed21574608
UniProtP39045|DAC_ACTSP D-alanyl-D-alanine carboxypeptidase (Gene Name=dac)

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