Structure of PDB 3r5x Chain D

Receptor sequence

>3r5xD (length=306) Species: 1392 (Bacillus anthracis)

NAMRIGVIMGGVSSEKQVSIMTGNEMIANLDKNKYEIVPITLNEKMDLIE
KAKDIDFALLALHGKYGEDGTVQGTLESLGIPYSGSNMLSSGICMDKNIS
KKILRYEGIETPDWIELTKMEDLNFDELDKLGFPLVVKPNSGGSSVGVKI
VYDKDELISMLETVFEWDSEVVIEKYIKGEEITCSIFDGKQLPIISIRHA
AEFFDYNAKYDDASTIEEVIELPAELKERVNKASLACYKALKCSVYARVD
MMVKDGIPYVMEVNTLPGMTQASLLPKSADAAGIHYSKLLDMIIETSLRV
RKEEGF

3D structure

• PDB: 3r5x Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis complexed with ATP
• Chain: D
• Resolution: 2.0 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): E13 V16 M19 H61 S142 N205 Y208 R246 D248 E260 N262 G266 A270
• Catalytic site (residue number reindexed from 1): E15 V18 M21 H63 S144 N207 Y210 R248 D250 E262 N264 G268 A272
• Enzyme Commision number: 6.3.2.4: D-alanine--D-alanine ligase.

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	CA	D	D248 E260	D250 E262
BS02	ATP	D	V134 K136 V146 E172 Y174 I175 E179 M250 M259 E260 N262	V136 K138 V148 E174 Y176 I177 E181 M252 M261 E262 N264
BS03	CA	D	E200 D203 Y208	E202 D205 Y210

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0005524 ATP binding
• GO:0008716 D-alanine-D-alanine ligase activity
• GO:0016874 ligase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0008360 regulation of cell shape
• GO:0009252 peptidoglycan biosynthetic process
• GO:0071555 cell wall organization

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3r5x, PDBe:3r5x, PDBj:3r5x
• PDBsum: 3r5x
• UniProt: Q81Q29|DDL_BACAN D-alanine--D-alanine ligase (Gene Name=ddl)