Structure of PDB 4c5b Chain A Binding Site BS06

Receptor Information

>4c5b Chain A (length=306) Species: 83333 (Escherichia coli K-12)

MTDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQL
KSMGFQKVFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRS
KLLWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGS
SVGMSKVVAENALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPS
IRIQPSGTFYDYEAKYLSDETQYFCPAGLEASQEANLQALVLKAWTTLGC
KGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVR
ILELAD

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 4c5b Chain A Residue 1314

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4c5b Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): D257 E270
• Binding residue (residue number reindexed from 1): D257 E270
• Annotation score: 1

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): E15 V18 N21 H63 S150 E213 Y216 R255 D257 E270 N272 G276 H280
• Enzyme Commision number: 6.3.2.4: D-alanine--D-alanine ligase.

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:4c5b, PDBe:4c5b, PDBj:4c5b
• PDBsum: 4c5b
• PubMed: 29208891
• UniProt: P07862|DDLB_ECOLI D-alanine--D-alanine ligase B (Gene Name=ddlB)