Structure of PDB 6knc Chain B Binding Site BS03

Receptor Information
>6knc Chain B (length=1118) Species: 311400 (Thermococcus kodakarensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PEMKAYFESLQREIDRAYAIARKARAQGKDPSFDVEVPQATDMAGRVESL
VGPPGVAERIRELVKEYGKEIAALKVVDEIIEGKFGDLGSKEKYAEQAVR
TALAILTEGIVSAPLEGIADVKIKRNEWADGSEYLALYYAGPIRSSGGTA
QALSVLVGDYVRRKLGLDRFKPSDEHIERMVEEVDLYHRAVTRLQYHPEA
DEVRLAMRNIPIEITGEETDKVEVSHRNVPGVETNHLRGGAILVLAEGVL
QKAKKLVKYIDKMGIEGWDWIKEFVEAKEKGVEKGFYYELYEKFRANIAP
NKKYTKEIIGGRPLFAEPSTNGGFRLRYGRSWSVNPATMLILGCIVTPAT
TVEGPIVRLKNGSVVRVDDYETALKVRNEVDEILYVGDALVNFGDFVENN
QTLLPANYVEEWWVQELVQAIKDLYEVELQPFAENDREAVEEAAEYLEVD
PDFLWNLLKDPLRVKPDVETAIHLSTVLDIPFHPYYTLYWNTLQPEEVEE
LQKALLGAQIEWAEFRKNRFAKKVVLENDKNIKRYLELLGLPHRLERVEK
KRKVIVVEYPWSAALLTPLGNLEWEFKAKPFYTVIDIINENNRIKLRDRG
ISWIGKPPVQVLFPIGLAGGQSRDIKKAAEEGKTARVEIAFFKCPKCGHV
GPEHLCPVCGTRKELLWHCPKCGADYPESDAKDFNYRCPKCDVELKPYAE
REIKPADLLRQAMDNVKVYGIDRLKGVKGMTSGYKMAEPLEKGLLRVKND
VYVFKDGTIRFDATDAPITHFKPKEIGTSVEKLRELGYTHDFEGKPLERD
DQILELKVQDVILPYEAGRYLLKVARFIDDLLEKFYGLPRFYNAEKMEDL
VGHLVIGLAPHTSAGIIGRIIGFSDVLVGYAHPYYHAAKRRNCDGDEDAV
MLLLDALLNFSKYYLPEKRGGKMDAPLVVTTRLDPREVDSEVHNMDVVRY
YPLEFYKATYELKSPKEVKVIERVEDGDMEEKVARQLALAERIRAVDEHH
VAETIINSHLVPDLRGNLRSFTRQEFRCVKCNTKYRRPPLTGKCPKCGGK
IVLTVSKGAIEKYLPTAKMLVTKYRVKDYTRQRICITEKDIKTLFQRTLM
GFSADICEKMVKERTGHS
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain6knc Chain B Residue 1401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6knc Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy.
Resolution9.3 Å
Binding residue
(original residue number in PDB)		C715 C718 C727 C730
Binding residue
(residue number reindexed from 1)		C644 C647 C656 C659
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
3.1.11.1: exodeoxyribonuclease I.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:0006260 DNA replication

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:6knc, PDBe:6knc, PDBj:6knc
PDBsum6knc
PubMed33115459
UniProtQ5JET0|DP2L_THEKO DNA polymerase II large subunit (Gene Name=polC)

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