Structure of PDB 3vmm Chain A Binding Site BS01

Receptor Information

>3vmm Chain A (length=471) Species: 1423 (Bacillus subtilis)

ERKTVLVIADLGGCPPHMFYKSAAEKYNLVSFIPRPFAITASHAALIEKY
SVAVIKDKDYFKSLADFEHPDSIYWAHEDHNKPEEEVVEQIVKVAEMFGA
DAITTNNELFIAPMAKACERLGLRGAGVQAAENARDKNKMRDAFNKAGVK
SIKNKRVTTLEDFRAALEEIGTPLILKPTYLASSIGVTLITDTETAEDEF
NRVNDYLKSINVPKAVTFEAPFIAEEFLQGEYGDWYQTEGYSDYISIEGI
MADGEYFPIAIHDKTPQIGFTETSHITPSILDEEAKKKIVEAAKKANEGL
GLQNCATHTEIKLMKNREPGLIESAARFAGWNMIPNIKKVFGLDMAQLLL
DVLCFGKDADLPDGLLDQEPYYVADCHLYPQHFKQNGQIPETAEDLVIEA
IDIPDGLLKGDTEIVSFSAAAPGTSVDLTLFEAFNSIAAFELKGSNSQDV
AESIRQIQQHAKLTAKYVLPV

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: 3vmm Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3vmm Structural and enzymatic characterization of BacD, an l-amino acid dipeptide ligase from Bacillus subtilis
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): E311 E324
• Binding residue (residue number reindexed from 1): E310 E323
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 6.3.2.49: L-alanine--L-anticapsin ligase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0005524 ATP binding
• GO:0016874 ligase activity
• GO:0034026 L-amino-acid alpha-ligase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0017000 antibiotic biosynthetic process

External links

• PDB: RCSB:3vmm, PDBe:3vmm, PDBj:3vmm
• PDBsum: 3vmm
• PubMed: 22407814
• UniProt: P39641|BACD_BACSU Alanine--anticapsin ligase (Gene Name=bacD)