Structure of PDB 3ekg Chain B Binding Site BS01

Receptor Information

>3ekg Chain B (length=395) Species: 322710 (Azotobacter vinelandii DJ)

SLSIPTIKQVRAFVLRGGGADYHDQGDGHWIDDHISTPMGKYPEYRQSRR
SFGINVLGTLVVEIEASDGNVGFAVTTGGEPAAYIVEKHLARFLEGARVT
DIERIWDQMYNSTLYYGRKGLVINTISGVDLALWDLLGKVRREPVHQLLG
GAVRDELQFYATGARPDLAQKMGFIGGKMPLHHGPSEGEEGLKKNLEELA
TMRERVGPDFWLMFDCWMSLDLNYATRLARGAREYGLKWIEEALPPDDYW
GYAELRRNAPTGMMVTTGEHEATRWGFRMLLEMGCCDIIQPDVGWCGGVT
ELLKISALADAHNALVVPHGSSVYSYHFVATRQNSPFAEFLMMAPKADQV
VPMFHPQLLGEPVPENGRMRLSRLDQPGFGVTLNPECQLHRPYTH

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: 3ekg Chain B Residue 602

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3ekg CRYSTAL STRUCTURE OF L-RHAMNONATE DEHYDRATASE FROM AZOTOBACTER VINELANDII complexed with Mg and L-TARTRATE
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): D216 E242 E270
• Binding residue (residue number reindexed from 1): D215 E241 E269
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K179 P181 G185 S187 E191 D216 W218 E242 T267 G269 E270 Q291 D293 H320 E340 D349
• Catalytic site (residue number reindexed from 1): K178 P180 G184 S186 E190 D215 W217 E241 T266 G268 E269 Q290 D292 H319 E339 D348
• Enzyme Commision number: 4.2.1.90: L-rhamnonate dehydratase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0016829 lyase activity
• GO:0016836 hydro-lyase activity
• GO:0046872 metal ion binding
• GO:0050032 L-rhamnonate dehydratase activity

Biological Process

• GO:0009063 amino acid catabolic process
• GO:0016052 carbohydrate catabolic process

External links

• PDB: RCSB:3ekg, PDBe:3ekg, PDBj:3ekg
• PDBsum: 3ekg
• UniProt: C1DMY1