Structure of PDB 6knb Chain B

Receptor sequence
>6knbB (length=1120) Species: 311400 (Thermococcus kodakarensis) [Search protein sequence]
PEMKAYFESLQREIDRAYAIARKARAQGKDPSFDVEVPQATDMAGRVESL
VGPPGVAERIRELVKEYGKEIAALKVVDEIIEGKFGDLGSKEKYAEQAVR
TALAILTEGIVSAPLEGIADVKIKRNEWADGSEYLALYYAGPIRSSGGTA
QALSVLVGDYVRRKLGLDRFKPSDEHIERMVEEVDLYHRAVTRLQYHPEA
DEVRLAMRNIPIEITGEETDKVEVSHRNVPGVETNHLRGGAILVLAEGVL
QKAKKLVKYIDKMGIEGWDWIKEFVEAKEKGVEKGFYYELYEKFRANIAP
NKKYTKEIIGGRPLFAEPSTNGGFRLRYGRSWSVNPATMLILGCIVTPAT
TVEGPIVRLKNGSVVRVDDYETALKVRNEVDEILYVGDALVNFGDFVENN
QTLLPANYVEEWWVQELVQAIKDLYEVELQPFAENDREAVEEAAEYLEVD
PDFLWNLLKDPLRVKPDVETAIHLSTVLDIPFHPYYTLYWNTLQPEEVEE
LQKALLGAQIEWAEFRKNRFAKKVVLENDKNIKRYLELLGLPHRLERVEK
KRKVIVVEYPWSAALLTPLGNLEWEFKAKPFYTVIDIINENNRIKLRDRG
ISWIGKPPVQVLFPIGLAGGQSRDIKKAAEEGKTARVEIAFFKCPKCGHV
GPEHLCPVCGTRKELLWHCPKCGADYPESDAKDFNYRCPKCDVELKPYAE
REIKPADLLRQAMDNVKVYGIDRLKGVKGMTSGYKMAEPLEKGLLRVKND
VYVFKDGTIRFDATDAPITHFKPKEIGTSVEKLRELGYTHDFEGKPLERD
DQILELKVQDVILPYEAGRYLLKVARFIDDLLEKFYGLPRFYNAEKMEDL
VGHLVIGLAPHTSAGIIGRIIGFSDVLVGYAHPYYHAAKRRNCDGDEDAV
MLLLDALLNFSKYYLPEKRGGKMDAPLVVTTRLDPREVDSEVHNMDVVRY
YPLEFYKATYELKSPKEVKVIERVEDGDMEEKVARQLALAERIRAVDEHH
VAETIINSHLVPDLRGNLRSFTRQEFRCVKCNTKYRRPPLTGKCPKCGGK
IVLTVSKGAIEKYLPTAKMLVTKYRVKDYTRQRICITEKDIKTLFEKQRT
LMGFSADICEKMVKERTGHS
3D structure
PDB6knb Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy.
ChainB
Resolution6.9 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
3.1.11.1: exodeoxyribonuclease I.
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 B Q692 R794 P1115 Q621 R723 P1012
BS02 dna B G1080 E1084 A1162 K1165 G977 E981 A1059 K1062
BS03 ZN B C715 C718 C727 C730 C644 C647 C656 C659
BS04 ZN B C1131 C1134 C1028 C1031
BS05 ZN B C740 C743 C759 C669 C672 C688
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:0006260 DNA replication

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Molecular Function
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Biological Process
External links
PDB RCSB:6knb, PDBe:6knb, PDBj:6knb
PDBsum6knb
PubMed33115459
UniProtQ5JET0|DP2L_THEKO DNA polymerase II large subunit (Gene Name=polC)

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