Structure of PDB 3eph Chain B Binding Site BS03

Receptor Information
>3eph 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 IDPPV
InChIInChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)
InChIKeyXPPKVPWEQAFLFU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OP(=O)(O)O
CACTVS 3.341O[P](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.5.0OP(=O)(O)OP(=O)(O)O
FormulaH4 O7 P2
NamePYROPHOSPHATE
ChEMBLCHEMBL1160571
DrugBankDB04160
ZINCZINC000006827695
PDB chain3eph 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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PDB3eph Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism.
Resolution2.95 Å
Binding residue
(original residue number in PDB)		T23 G24 G26 K27 S28 N59
Binding residue
(residue number reindexed from 1)		T11 G12 G14 K15 S16 N47
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3eph, PDBe:3eph, PDBj:3eph
PDBsum3eph
PubMed18852462
UniProtP07884|MOD5_YEAST tRNA dimethylallyltransferase (Gene Name=MOD5)

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