Structure of PDB 8d9d Chain C

Receptor sequence

>8d9dC (length=1058) Species: 9606 (Homo sapiens)

EQVFHFYWLDAYEDQYNQPGVVFLFGKVWIESAETHVSCCVMVKNIERTL
YFLPREMKIDLNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKSKPVEK
NYAFEIPDVPEKSEYLEVKYSAEMPQLPQDLKGETFSHVFGTNTSSLELF
LMNRKIKGPCWLEVKSPQLLNQPVSWCKVEAMALKPDLVNVIKDVSPPPL
VVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQSHFCVVS
KPKDCIFPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGH
NIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGFGERNATCGRMIC
DVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYL
LEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFL
LLHAFYENNYIVPDKQIAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSII
QEFNICFTTVQRVEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQ
DLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGRE
ILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKL
YKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYVTKQELKGLDIVRR
DWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQ
FEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQD
GSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGIDA
VLIATWLGLDPTQFRVHHYTDEEKYRDCERFKCPCPTCGTENIYDNVFDG
SGTDMEPSLYRCSNIDCKASPLTFTVQLSNKLIMDIRRFIKKYYDGWLIC
EEPTCRNRTRHLPLQFSRTGPLCPACMKATLQPEYSDKSLYTQLCFYRYI
FDAECALEKLTTDHEKDKLKKQFFTPKVLQDYRKLKNTAEQFLSRSGYSE
VNLSKLFA

3D structure

• PDB: 8d9d Structures of human primosome elongation complexes.
• Chain: C
• Resolution: 3.59 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	rna	C	D1002 K1075 R1081 R1082 A1138 T1140 K1141 L1152 H1154	D620 K693 R699 R700 A756 T758 K759 L770 H772
BS02	dna	C	G783 R784 A837 G841 V844 G958 F962 Y964 K1051 K1054 R1222	G442 R443 A468 G472 V475 G576 F580 Y582 K669 K672 R840
BS03	MG	C	D860 F861 D1004	D491 F492 D622
BS04	ZN	C	C1283 C1286 C1310 C1315	C885 C888 C912 C917
BS05	ZN	C	C1348 C1353 C1371 C1374	C950 C955 C973 C976
BS06	DTP	C	S863 Y865 R922 K950 D1004	S494 Y496 R540 K568 D622

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003682 chromatin binding
• GO:0003688 DNA replication origin binding
• GO:0003697 single-stranded DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0019901 protein kinase binding
• GO:0046872 metal ion binding

Biological Process

• GO:0000731 DNA synthesis involved in DNA repair
• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0006269 DNA replication, synthesis of primer
• GO:0006270 DNA replication initiation
• GO:0006271 DNA strand elongation involved in DNA replication
• GO:0006272 leading strand elongation
• GO:0006273 lagging strand elongation
• GO:0006281 DNA repair
• GO:0006289 nucleotide-excision repair
• GO:0006303 double-strand break repair via nonhomologous end joining
• GO:0032479 regulation of type I interferon production
• GO:1902975 mitotic DNA replication initiation
• GO:1904161 DNA synthesis involved in UV-damage excision repair

Cellular Component

• GO:0000785 chromatin
• GO:0005634 nucleus
• GO:0005635 nuclear envelope
• GO:0005654 nucleoplasm
• GO:0005658 alpha DNA polymerase:primase complex
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0016363 nuclear matrix
• GO:0031981 nuclear lumen

External links

• PDB: RCSB:8d9d, PDBe:8d9d, PDBj:8d9d
• PDBsum: 8d9d
• PubMed: 37069376
• UniProt: P09884|DPOLA_HUMAN DNA polymerase alpha catalytic subunit (Gene Name=POLA1)