Structure of PDB 4i2j Chain A Binding Site BS01

Receptor Information
>4i2j Chain A (length=353) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVL
KSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKS
FKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYED
LVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFLI
TSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKFKQPDALDHFQ
KCFLILKLDHGRVHSEKGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFE
RDLRRYATHERKMMLDNHALYDRTKRVFLEAESEEEIFAHLGLDYIEPWE
RNA
Ligand information
Ligand IDDCP
InChIInChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyRGWHQCVHVJXOKC-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
FormulaC9 H16 N3 O13 P3
Name2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL560403
DrugBankDB03258
ZINCZINC000008215945
PDB chain4i2j Chain A Residue 601 [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]
PDB4i2j Structures of Intermediates along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		G332 G333 R336 G341 H342 D343 D345 G449 W450 R454
Binding residue
(residue number reindexed from 1)		G184 G185 R188 G193 H194 D195 D197 G292 W293 R297
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D343 D345 D434
Catalytic site (residue number reindexed from 1) D195 D197 D277
Enzyme Commision number 2.7.7.31: DNA nucleotidylexotransferase.
3.1.11.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0016779 nucleotidyltransferase activity
GO:0034061 DNA polymerase activity
Biological Process
GO:0006281 DNA repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4i2j, PDBe:4i2j, PDBj:4i2j
PDBsum4i2j
PubMed23856622
UniProtP09838|TDT_MOUSE DNA nucleotidylexotransferase (Gene Name=Dntt)

[Back to BioLiP]