Structure of PDB 3dst Chain B Binding Site BS01

Receptor Information
>3dst Chain B (length=325) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QKDVTIKSDAPDTLLLEKHADYIASYGSKDYEYCMSEYLRMSGVYWGLTV
MDLMGQLHRMNKEEILVFIKSCQHECGGVSASIGHDPHLLYTLSAVQILT
LYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAVATLALL
GKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQ
LHQVNSDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLH
WIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSLLGEEQI
KPVSPVFCMPEEVLQRVNVQPELVS
Ligand information
Ligand IDGRG
InChIInChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)/b18-11+,19-13+,20-15+
InChIKeyOINNEUNVOZHBOX-QIRCYJPOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)=CCCC(/C)=C/CC\C(C)=C\CC\C(C)=C\CO[P](O)(=O)O[P](O)(O)=O
CACTVS 3.385CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCO[P](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.7.5CC(=CCCC(=CCCC(=CCCC(=CCOP(=O)(O)OP(=O)(O)O)C)C)C)C
OpenEye OEToolkits 1.7.5CC(=CCC/C(=C/CC/C(=C/CC/C(=C/CO[P@](=O)(O)OP(=O)(O)O)/C)/C)/C)C
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OC/C=C(/CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)C)C
FormulaC20 H36 O7 P2
NameGERANYLGERANYL DIPHOSPHATE
ChEMBLCHEMBL1229266
DrugBank
ZINCZINC000012495043
PDB chain3dst Chain B Residue 334 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3dst Structures of RabGGTase-substrate/product complexes provide insights into the evolution of protein prenylation
Resolution1.9 Å
Binding residue
(original residue number in PDB)		H190 G192 C196 R232 K235 Y241 W244 F293
Binding residue
(residue number reindexed from 1)		H184 G186 C190 R226 K229 Y235 W238 F287
Annotation score5
Binding affinityMOAD: Kd=0.83nM
PDBbind-CN: -logKd/Ki=9.08,Kd=0.83nM
Enzymatic activity
Catalytic site (original residue number in PDB) H190 R232 K235 D238 C240 Y241 D280 D287 H290
Catalytic site (residue number reindexed from 1) H184 R226 K229 D232 C234 Y235 D274 D281 H284
Enzyme Commision number 2.5.1.60: protein geranylgeranyltransferase type II.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004659 prenyltransferase activity
GO:0004661 protein geranylgeranyltransferase activity
GO:0004663 Rab geranylgeranyltransferase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0008318 protein prenyltransferase activity
GO:0019840 isoprenoid binding
GO:0031267 small GTPase binding
GO:0046872 metal ion binding
Biological Process
GO:0018344 protein geranylgeranylation
Cellular Component
GO:0005968 Rab-protein geranylgeranyltransferase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3dst, PDBe:3dst, PDBj:3dst
PDBsum3dst
PubMed18756270
UniProtQ08603|PGTB2_RAT Geranylgeranyl transferase type-2 subunit beta (Gene Name=Rabggtb)

[Back to BioLiP]