Structure of PDB 2dvi Chain A Binding Site BS03

Receptor Information
>2dvi Chain A (length=431) Species: 2234 (Archaeoglobus fulgidus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNT
WLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHG
VVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLK
GFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVID
VAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLG
FFKPKIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFE
FLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVK
KFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGE
SIREYFEIISGEKLFKEPVTAELCEMMGVKD
Ligand information
Ligand IDCTP
InChIInChI=1S/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyPCDQPRRSZKQHHS-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
FormulaC9 H16 N3 O14 P3
NameCYTIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL223533
DrugBankDB02431
ZINCZINC000003861746
PDB chain2dvi Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2dvi Complete crystallographic analysis of the dynamics of CCA sequence addition
Resolution2.61 Å
Binding residue
(original residue number in PDB)		S47 R50 D61 T130 H133 K152 Y161
Binding residue
(residue number reindexed from 1)		S45 R48 D59 T128 H131 K150 Y159
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.7.72: CCA tRNA nucleotidyltransferase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000287 magnesium ion binding
GO:0003723 RNA binding
GO:0004810 CCA tRNA nucleotidyltransferase activity
GO:0005524 ATP binding
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
GO:0160016 CCACCA tRNA nucleotidyltransferase activity
Biological Process
GO:0001680 tRNA 3'-terminal CCA addition
GO:0008033 tRNA processing
GO:0031123 RNA 3'-end processing
GO:0042245 RNA repair
GO:0106354 tRNA surveillance

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2dvi, PDBe:2dvi, PDBj:2dvi
PDBsum2dvi
PubMed17051158
UniProtO28126|CCA_ARCFU CCA-adding enzyme (Gene Name=cca)

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