Structure of PDB 7u9k Chain B Binding Site BS02

Receptor Information

>7u9k Chain B (length=330) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

ENICIVFGGKSAEHEVSILTAQNVLNAIYHVDIIYITNDGDWRKQNNITA
EIKSTDELHLEISQLLQPYDAVFPLLHGPNGEDGTIQGLFEVLDVPYVGN
GVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVNDK
LNYPVFVKPANLGSSVGISKCNNEAELKEGIKEAFQFDRKLVIEQGVNAR
EIEVAVLGNDYPEATWPGEVVKDVAFYDYKSKYKDGKVQLQIPADLDEDV
QLTLRNMALEAFKATDCSGLVRADFFVTEDNQIYINETNAMPGFTAFSMY
PKLWENMGLSYPELITKLIELAKERHQDKQ

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: 7u9k Chain B Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7u9k Staphylococcus aureus D-alanine-D-alanine ligase in complex with ATP, D-ala-D-ala, Mg2+ and K+
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): E306 N308
• Binding residue (residue number reindexed from 1): E287 N289
• Annotation score: 1

Enzymatic activity

• 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: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:7u9k, PDBe:7u9k, PDBj:7u9k
• PDBsum: 7u9k
• PubMed: 37948922
• UniProt: Q2FWH3|DDL_STAA8 D-alanine--D-alanine ligase (Gene Name=ddl)