Structure of PDB 3zvw Chain B

Receptor sequence

>3zvwB (length=465) Species: 72570 (Actinomadura sp. R39)

RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASN
MKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSA
EDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQ
ISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTG
AAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFE
EALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNN
GHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLS
RGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRG
TAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQD
AIAVRLAEYAGHQAP

3D structure

• PDB: 3zvw Unexpected Tricovalent Binding Mode of Boronic Acids within the Active Site of a Penicillin- Binding Protein.
• Chain: B
• Resolution: 2.0 Å

Enzymatic activity

• Enzyme Commision number: 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	FP5	B	A48 S49 S298 N300 G348 L349 K410 T411 G412 T413	A48 S49 S298 N300 G348 L349 K410 T411 G412 T413	PDBbind-CN: -logKd/Ki=3.90,Ki=125uM BindingDB: Ki=125000nM,IC50=320000nM
BS02	33D	B	W139 M414 S415	W139 M414 S415

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

External links

• PDB: RCSB:3zvw, PDBe:3zvw, PDBj:3zvw
• PDBsum: 3zvw
• PubMed: 21574608
• UniProt: P39045|DAC_ACTSP D-alanyl-D-alanine carboxypeptidase (Gene Name=dac)