Structure of PDB 3dyf Chain B

Receptor sequence

>3dyfB (length=358) Species: 5691 (Trypanosoma brucei)

MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNR
GLTVIDVAESLLSLDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNS
VTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLC
RFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIV
KYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMD
CFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEK
VATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLW
GKTYKRQK

3D structure

• PDB: 3dyf Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation.
• Chain: B
• Resolution: 2.65 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K47 H98 D103 D107 R112 D175 K212 F251 D255 D256
• Catalytic site (residue number reindexed from 1): K47 H89 D94 D98 R103 D166 K203 F242 D246 D247
• Enzyme Commision number: 2.5.1.10: (2E,6E)-farnesyl diphosphate synthase.

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	MG	B	D103 D107	D94 D98
BS02	MG	B	D103 D107 D175	D94 D98 D166
BS03	NI9	B	D103 D107 R112 Q172 K212 D255 K269	D94 D98 R103 Q163 K203 D246 K260
BS04	IPR	B	K47 R50 Q96 R113 F251 D255	K47 R50 Q87 R104 F242 D246

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

External links

• PDB: RCSB:3dyf, PDBe:3dyf, PDBj:3dyf
• PDBsum: 3dyf
• PubMed: 19309137
• UniProt: Q86C09