Structure of PDB 4oi4 Chain C Binding Site BS02

Receptor Information
>4oi4 Chain C (length=427) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GDNEWHKLVIPKGSDWQIDLKAEGKLIVKVNSGIVEIFGTELAVDDEYTF
QNWKFPIYAVEETELLWKCPDLTTNTITVKPNHTMKYIYNLHFMLEKIRM
SNFEGPRVVIVGGSQTGKTSLSRTLCSYALKFNAYQPLYINLDPQQPIFT
VPGCISATPISDILDAQLPTWGQSLTSGATLLHNKQPMVKNFGLERINEN
KDLYLECISQLGQVVGQRLHLDPQVRRSGCIVDTPSISQLDENLAELHHI
IEKLNVNIMLVLCSETDPLWEKVKKTFGPELGNNNIFFIPKLDGVSAVDD
VYKRSLQRTSIREYFYGSLDTALSPYAIGVDYEDLTIWKPSNVFDNEVGR
VELFPVTITPSNLQHAIIAITFAERRADQATVIKSPILGFALITEVNEKR
RKLRVLLPVPGRLPSKAMILTSYRYLE
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain4oi4 Chain C Residue 501 [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]
PDB4oi4 RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D33 Q35 K72 P74 Q133 G135 K136 T137 S138 G312 V313 S314
Binding residue
(residue number reindexed from 1)		D15 Q17 K54 P56 Q115 G117 K118 T119 S120 G294 V295 S296
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.1.78: polynucleotide 5'-hydroxyl-kinase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0051731 polynucleotide 5'-hydroxyl-kinase activity
Biological Process
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation
GO:0006396 RNA processing
GO:0006397 mRNA processing
GO:0031124 mRNA 3'-end processing
Cellular Component
GO:0005634 nucleus
GO:0005849 mRNA cleavage factor complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4oi4, PDBe:4oi4, PDBj:4oi4
PDBsum4oi4
PubMed24813946
UniProtQ08685|CLP1_YEAST mRNA cleavage and polyadenylation factor CLP1 (Gene Name=CLP1)

[Back to BioLiP]