Structure of PDB 3ryw Chain A

Receptor sequence

>3rywA (length=358) Species: 126793 (Plasmodium vivax Sal-1)

LAFFRNMYDKYRDAFLSHLNEYSLEEEIKEHISKYYKLLFDYNCLGGKNN
RGILVILIYEYVKNRINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEM
RRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATF
RDATLKTIIGQHLDTNIFSDKYSEIDVNNINVPEQPVIDINMINFGVYKN
IVIHKTAYYSFFLPIVCGMLLAGIAVDNLIYKKIEDISMLMGEYFQIHDD
YLDIFGDSTKTGKVGSDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNN
LACVKVIDSLYEQYKIRKHYESYEKAQKAKILSAINELHHEGIEYVLKYL
LEILFTGV

3D structure

• PDB: 3ryw Lipophilic analogs of zoledronate and risedronate inhibit Plasmodium geranylgeranyl diphosphate synthase (GGPPS) and exhibit potent antimalarial activity.
• Chain: A
• Resolution: 2.9 Å

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

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	K9H	A	F122 A125 D126 R135 Q195 K243 D287 K301	F88 A91 D92 R101 Q161 K205 D249 K263	PDBbind-CN: -logKd/Ki=6.24,Ki=570nM
BS02	MG	A	D126 D130	D92 D96
BS03	MG	A	D126 D130 Q195	D92 D96 Q161
BS04	K9H	A	V153 L157	V119 L123	PDBbind-CN: -logKd/Ki=6.24,Ki=570nM

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:3ryw, PDBe:3ryw, PDBj:3ryw
• PDBsum: 3ryw
• PubMed: 22392982
• UniProt: A5K4U6