Structure of PDB 2xdm Chain A Binding Site BS02

Receptor Information
>2xdm Chain A (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 IDCO
InChIInChI=1S/Co/q+2
InChIKeyXLJKHNWPARRRJB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Co+2]
CACTVS 3.341[Co++]
FormulaCo
NameCOBALT (II) ION
ChEMBL
DrugBankDB14205
ZINC
PDB chain2xdm Chain A Residue 611 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2xdm Crystal Structure of a Complex between the Actinomadura R39 Dd-Peptidase and a Peptidoglycan- Mimetic Boronate Inhibitor: Interpretation of a Transition State Analogue in Terms of Catalytic Mechanism.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		A402 H462
Binding residue
(residue number reindexed from 1)		A402 H462
Annotation score1
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:2xdm, PDBe:2xdm, PDBj:2xdm
PDBsum2xdm
PubMed20608745
UniProtP39045|DAC_ACTSP D-alanyl-D-alanine carboxypeptidase (Gene Name=dac)

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