Structure of PDB 8v6i Chain A Binding Site BS05

Receptor Information
>8v6i Chain A (length=1050) Species: 8355 (Xenopus laevis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVFRFYWLDAYEDQYSQPGVVYLFGKVWIESADAYVSCCVSVKNIERTVY
LLPRENRVQLSTGKDTGAPVSMMHVYQEFNEAVAEKYKIMKFKSKKVDKD
YAFEIPDVPASSEYLEVRYSADSPQLPQDLKGETFSHVFGTNTSSLELFL
LSRKIKGPSWLEIKSPQLSSQPMSWCKVEAVVTRPDQVSVVKDLAPPPVV
VLSLSMKTVQNAKTHQNEIVAIAALVHHTFPLDKAPPQPPFQTHFCVLSK
LNDCIFPYDYNEAVKQKNANIEIALTERTLLGFFLAKIHKIDPDVIVGHD
IYGFDLEVLLQRINSCKVPFWSKIGRLRRSVMPKLGGRSGFAERNAACGR
IICDIEISAKELIRCKSYHLSELVHQILKAERVVIPPENIRNAYNDSVHL
LYMLENTWIDAKFILQIMCELNVLPLALQITNIAGNVMSRTLMGGRSERN
EYLLLHAFTENNFIVPDKPVAAYAGGLVLEPKVGFYDKFILLLDFNSLYP
SIIQEYNICFTTVHREADEIPELPHSDLEMGILPREIRKLVERRRHVKQL
MKQPDLNPDLYLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTH
QGREILLHTKEMVQKMNLEVIYGDTDSIMINTNCNNLEEVFKLGNRVKSE
INKSYKLLEIDIDGIFKSLLLLKKKKYAALTVEPTGDGKYVTKQELKGLD
IVRRDWCELAKQAGNYVISQILSDQPRDSIVENIQKKLTEIGENVTNGTV
PITQYEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTISYV
ICQDGSNLSASQRAYAQEQLQKQENLSIDTQYYLSQQVHPVVARICEPID
GIDSALIAMWLGLDPSQFRDCERFKFFCPKCGTENIYDNVFDGSGLQIEP
GLKRCSKPECDASPLDYVIQVHNKLLLDIRRYIKKYYSGWLVCEEKTCQN
RTRRLPLSFSRNGPICQACSKATLRSEYPEKALYTQLCFYRFIFDWDYAL
EKVVSEQERGHLKKKLFQESENQYKKLKSTVDQVLSRSGYSEVNLSKLFQ
Ligand information
Ligand IDDGT
InChIInChI=1S/C10H16N5O13P3/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
InChIKeyHAAZLUGHYHWQIW-KVQBGUIXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H16 N5 O13 P3
Name2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL477486
DrugBankDB02181
ZINCZINC000008215755
PDB chain8v6i Chain A Residue 1503 [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]
PDB8v6i A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase
Resolution14.06 Å
Binding residue
(original residue number in PDB)		F860 N861 S862 Y864 R918 K946 N950 Y953 D1000
Binding residue
(residue number reindexed from 1)		F495 N496 S497 Y499 R544 K572 N576 Y579 D626
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:0006260 DNA replication
GO:1902975 mitotic DNA replication initiation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8v6i, PDBe:8v6i, PDBj:8v6i
PDBsum8v6i
PubMed38491139
UniProtQ9DE46|DPOLA_XENLA DNA polymerase alpha catalytic subunit (Gene Name=pola1)

[Back to BioLiP]