Structure of PDB 3rbm Chain A Binding Site BS01

Receptor Information

>3rbm Chain A (length=355) Species: 126793 (Plasmodium vivax Sal-1)

LAFFRNMYDKYRDAFLSHLNEYSLEEEIKEHISKYYKLLFDYNCLGGKNN
RGILVILIYEYVKNRINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEM
RRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATF
RDATLKTIIGQHLDTNIFSDKYSEIDVNNINVPEQPVIDINMINFGVYKN
IVIHKTAYYSFFLPIVCGMLLAGIAVDNLIYKKIEDISMLMGEYFQIHDD
YLDIFGDSTKTGKVGSDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNN
LACVKVIDSLYEQYKIRKHYESYEKAQKAKILSAINELHHEGIEYVLKYL
LEILF

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: 3rbm Chain A Residue 1002

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3rbm Lipophilic analogs of zoledronate and risedronate inhibit Plasmodium geranylgeranyl diphosphate synthase (GGPPS) and exhibit potent antimalarial activity.
• Resolution: 2.61 Å
• Binding residue (original residue number in PDB): D126 D130
• Binding residue (residue number reindexed from 1): D92 D96
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K81 A121 D126 D130 R135 D198 K243 F283 D287 D288
• Catalytic site (residue number reindexed from 1): K48 A87 D92 D96 R101 D164 K205 F245 D249 D250

Gene Ontology

Molecular Function

• GO:0004161 dimethylallyltranstransferase activity
• GO:0004337 geranyltranstransferase activity
• GO:0004659 prenyltransferase activity
• GO:0016740 transferase activity
• GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
• GO:0046872 metal ion binding

Biological Process

• GO:0008299 isoprenoid biosynthetic process
• GO:0045337 farnesyl diphosphate biosynthetic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0016020 membrane

External links

• PDB: RCSB:3rbm, PDBe:3rbm, PDBj:3rbm
• PDBsum: 3rbm
• PubMed: 22392982
• UniProt: A5K4U6