Structure of PDB 4ben Chain A

Receptor sequence

>4benA (length=466) Species: 72570 (Actinomadura sp. R39)

RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASN
MKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSA
EDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQ
ISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTG
AAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFE
EALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNN
GHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLS
RGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRG
TAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQD
AIAVRLAEYAGHQAPE

3D structure

• PDB: 4ben Crystal Structures of R39-Imipenem Acyl-Enzyme.
• Chain: A
• Resolution: 2.15 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	IM2	A	S49 S298 N300 L349 T411 G412	S49 S298 N300 L349 T411 G412
BS02	MG	A	E188 H247 E251	E188 H247 E251
BS03	MG	A	A402 H462	A402 H462

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:4ben, PDBe:4ben, PDBj:4ben
• PDBsum: 4ben
• UniProt: P39045|DAC_ACTSP D-alanyl-D-alanine carboxypeptidase (Gene Name=dac)