Structure of PDB 2y55 Chain D

Receptor sequence
>2y55D (length=466) Species: 72570 (Actinomadura sp. R39) [Search protein sequence]
RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASN
MKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSA
EDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQ
ISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTG
AAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFE
EALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNN
GHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLS
RGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRG
TAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQD
AIAVRLAEYAGHQAPE
3D structure
PDB2y55 Unexpected Tricovalent Binding Mode of Boronic Acids within the Active Site of a Penicillin- Binding Protein.
ChainD
Resolution2.6 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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 D S49 K52 S298 N300 K410 T411 T413 M414 S49 K52 S298 N300 K410 T411 T413 M414 BindingDB: Ki=125000nM,IC50=320000nM
BS02 MG D E188 H247 E251 E188 H247 E251
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2y55, PDBe:2y55, PDBj:2y55
PDBsum2y55
PubMed21574608
UniProtP39045|DAC_ACTSP D-alanyl-D-alanine carboxypeptidase (Gene Name=dac)

[Back to BioLiP]