Structure of PDB 8v6i Chain A

Receptor sequence

>8v6iA (length=1050) Species: 8355 (Xenopus laevis)

QVFRFYWLDAYEDQYSQPGVVYLFGKVWIESADAYVSCCVSVKNIERTVY
LLPRENRVQLSTGKDTGAPVSMMHVYQEFNEAVAEKYKIMKFKSKKVDKD
YAFEIPDVPASSEYLEVRYSADSPQLPQDLKGETFSHVFGTNTSSLELFL
LSRKIKGPSWLEIKSPQLSSQPMSWCKVEAVVTRPDQVSVVKDLAPPPVV
VLSLSMKTVQNAKTHQNEIVAIAALVHHTFPLDKAPPQPPFQTHFCVLSK
LNDCIFPYDYNEAVKQKNANIEIALTERTLLGFFLAKIHKIDPDVIVGHD
IYGFDLEVLLQRINSCKVPFWSKIGRLRRSVMPKLGGRSGFAERNAACGR
IICDIEISAKELIRCKSYHLSELVHQILKAERVVIPPENIRNAYNDSVHL
LYMLENTWIDAKFILQIMCELNVLPLALQITNIAGNVMSRTLMGGRSERN
EYLLLHAFTENNFIVPDKPVAAYAGGLVLEPKVGFYDKFILLLDFNSLYP
SIIQEYNICFTTVHREADEIPELPHSDLEMGILPREIRKLVERRRHVKQL
MKQPDLNPDLYLQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTH
QGREILLHTKEMVQKMNLEVIYGDTDSIMINTNCNNLEEVFKLGNRVKSE
INKSYKLLEIDIDGIFKSLLLLKKKKYAALTVEPTGDGKYVTKQELKGLD
IVRRDWCELAKQAGNYVISQILSDQPRDSIVENIQKKLTEIGENVTNGTV
PITQYEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTISYV
ICQDGSNLSASQRAYAQEQLQKQENLSIDTQYYLSQQVHPVVARICEPID
GIDSALIAMWLGLDPSQFRDCERFKFFCPKCGTENIYDNVFDGSGLQIEP
GLKRCSKPECDASPLDYVIQVHNKLLLDIRRYIKKYYSGWLVCEEKTCQN
RTRRLPLSFSRNGPICQACSKATLRSEYPEKALYTQLCFYRFIFDWDYAL
EKVVSEQERGHLKKKLFQESENQYKKLKSTVDQVLSRSGYSEVNLSKLFQ

3D structure

• PDB: 8v6i A mechanistic model of primer synthesis from catalytic structures of DNA polymerase alpha-primase
• Chain: A
• Resolution: 14.06 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	S677 F679 G783 R784 S785 A837 Y838 A839 G840 G841 F958 K1047 K1049 S1185	S339 F341 G445 R446 S447 A472 Y473 A474 G475 G476 F584 K673 K675 S811
BS02	dna	A	D998 R1077 R1078 K1133 A1134 T1136 Y1142 K1145 H1150	D624 R703 R704 K759 A760 T762 Y768 K771 H776
BS03	ZN	A	C1280 C1283 C1307 C1312	C878 C881 C905 C910
BS04	ZN	A	C1345 C1350 C1368 C1371	C943 C948 C966 C969
BS05	DGT	A	F860 N861 S862 Y864 R918 K946 N950 Y953 D1000	F495 N496 S497 Y499 R544 K572 N576 Y579 D626
BS06	MG	A	D859 F860 D1000	D494 F495 D626

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

External links

• PDB: RCSB:8v6i, PDBe:8v6i, PDBj:8v6i
• PDBsum: 8v6i
• PubMed: 38491139
• UniProt: Q9DE46|DPOLA_XENLA DNA polymerase alpha catalytic subunit (Gene Name=pola1)