Structure of PDB 3epl Chain B Binding Site BS03

Receptor Information
>3epl Chain B (length=402) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKKVIVIAGTTGVGKSQLSIQLAQKFNGEVINSDSMQVYKDIPIITNKHP
LQEREGIPHHVMNHVDWSEEYYSHRFETECMNAIEDIHRRGKIPIVVGGT
HYYLQTLFNKRVDTKSSERKLTRKQLDILESTDPDVIYNTLVKCDPDIAT
KYHPNDYRRVQRMLEIYYKTGKKPSETFNEQKITLKFDTLFLWLYSKPEP
LFQRLDDRVDDMLERGALQEIKQLYEYYSQNKFTPEQCENGVWQVIGFKE
FLPWLTVKLEDCIERMKTRTRQYAKRQVKWIKKMLIPDIKGDIYLLDATD
LSQWDTNASQRAIAISNDFISNRPIKQERAPKALEELLSKGETTMKKLDD
WTHYTCNVCRNADGKNVVAIGEKYWKIHLGSRRHKSNLKRNTRQADFEKW
KI
Ligand information
Ligand IDDMA
InChIInChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h3H,4H2,1-2H3,(H,9,10)(H2,6,7,8)
InChIKeyCBIDRCWHNCKSTO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=CCOP(=O)(O)OP(=O)(O)O)C
ACDLabs 10.04O=P(OP(=O)(OC/C=C(/C)C)O)(O)O
OpenEye OEToolkits 1.5.0CC(=CCO[P@@](=O)(O)OP(=O)(O)O)C
CACTVS 3.341CC(C)=CCO[P@](O)(=O)O[P](O)(O)=O
CACTVS 3.341CC(C)=CCO[P](O)(=O)O[P](O)(O)=O
FormulaC5 H12 O7 P2
NameDIMETHYLALLYL DIPHOSPHATE
ChEMBLCHEMBL343480
DrugBankDB01785
ZINCZINC000008215740
PDB chain3epl Chain B Residue 422 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3epl Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		T23 G24 G26 K27 S28 N59 R220
Binding residue
(residue number reindexed from 1)		T11 G12 G14 K15 S16 N47 R208
Annotation score5
Enzymatic activity
Enzyme Commision number 2.5.1.75: tRNA dimethylallyltransferase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0046872 metal ion binding
GO:0052381 tRNA dimethylallyltransferase activity
Biological Process
GO:0006400 tRNA modification
GO:0008033 tRNA processing
Cellular Component
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3epl, PDBe:3epl, PDBj:3epl
PDBsum3epl
PubMed18852462
UniProtP07884|MOD5_YEAST tRNA dimethylallyltransferase (Gene Name=MOD5)

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