Structure of PDB 4c5a Chain B

Receptor sequence

>4c5aB (length=304) Species: 83333 (Escherichia coli K-12)

DKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQLKS
MGFQKVFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKL
LWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSV
GMSKVVAENALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIR
IQPSGTFYDYEAKYLSDETQYFCPAGLEASQEANLQALVLKAWTTLGCKG
WGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRIL
ELAD

3D structure

• PDB: 4c5a Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine.
• Chain: B
• Resolution: 1.65 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): E15 V18 N21 H63 S150 E213 Y216 R255 D257 E270 N272 G276 H280
• Catalytic site (residue number reindexed from 1): E13 V16 N19 H61 S148 E211 Y214 R253 D255 E268 N270 G274 H278
• 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	ADP	B	K97 I142 K144 G149 S151 M154 E180 W182 L183 E187 F209 Y210 M259 E270	K95 I140 K142 G147 S149 M152 E178 W180 L181 E185 F207 Y208 M257 E268
BS02	DS0	B	E15 H63 S150 K215 Y216 R255 E270 N272 G276	E13 H61 S148 K213 Y214 R253 E268 N270 G274
BS03	MG	B	E270 N272	E268 N270
BS04	MG	B	D257 E270	D255 E268

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:0042803 protein homodimerization 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
• GO:0005829 cytosol

External links

• PDB: RCSB:4c5a, PDBe:4c5a, PDBj:4c5a
• PDBsum: 4c5a
• PubMed: 29208891
• UniProt: P07862|DDLB_ECOLI D-alanine--D-alanine ligase B (Gene Name=ddlB)