Structure of PDB 8ppv Chain B Binding Site BS03

Receptor Information
>8ppv Chain B (length=1188) Species: 272844 (Pyrococcus abyssi GE5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PKEMEEYFEMLQREIDKAYEIAKKARAQGKDPSLDVEIPQATDMAGRVES
LVGPPGVAKRIRELVKEYGKEIAALKIVDEIIEGKFGDLGSREKYAEQAV
RTALAILTEGIVSAPIEGIANVKIKRNTWADNSEYLALYYAGPIRSSGGT
AQALSVLVGDYVRRKLGLDRFKPSEKHIERMVEEVDLYHRAVTRLQYHPS
PEEVRLAMRNIPIEITGEATDDVEVSHRDVPGVETNQLRGGAILVLAEGV
LQKAKKLVKYIDKMGIEGWEWLKEFVEAKEDMGFYYSLYQKFKEEIAPSD
KYAKEVIGGRPLFSDPSKPGGFRLRYGRSRASGFATWGINPATMILVDEF
LAIGTQLKTERPGKGAVVTPVTTIEGPIVKLKDGSVLRVDDYNLALKVRE
DVEEILYLGDAVIAFGDFVENNQTLLPANYCEEWWILEFVKALKEIYEVH
LEPFTENEEESIEEASDYLEIDPEFLKEMLRDPLRVKPPVELAIHFSEVL
GIPLHPYYTLYWNSVEPKDVEKLWRLLKNYAEIEWSNFRGIKFAKKIVIS
QEKLGDSKRTLELLGLPHTVRDGNVIVDYPWAAALLTPLGNLNWEFMAKP
LYATIDIINENNEIKLRDRGISWIGARMGRPEKAKERKMKPPVQVLFPIG
LAGGSSRDIKKAAEEGKVAEVEIAFFKCPKCGHVGPEHLCPNCGTRKELL
WVCPRCNAEYPESQAEGYNYTCPKCNVKLRPYAKRKIRPSELLNRAMENV
KVYGVDKLKGVMGMTSGWKMPEPLEKGLLRAKNDVYVFKDGTIRFDATDA
PITHFRPREIGVSVEKLRELGYTHDFEGKPLVSEDQIVELKPQDIILSKE
AGRYLLKVAKFVDDLLEKFYGLPRFYNAEKMEDLIGHLVIGLAPHTSAGI
VGRIIGFVDALVGYAHPYFHAAKRRNCDGDEDAVMLLLDALLNFSRYYLP
EKRGGKMDAPLVITTRLDPREVDSEVHNMDIVRYYPLEFYEATYELKSPK
ELVGVIERVEDRLGKPEMYYGLKFTHDTDDIALGPKMSLYKQLGDMEEKV
RRQLEVAKRIRAVDEHGVAEKILNSHLIPDLRGNLRSFTRQEFRCVKCNT
KFRRPPLNGKCPVCGGKIVLTVSKGAIEKYLGTAKMLVTEYNVKNYTRQR
ICLTERDIDSLFENVFPETQLTLIVNPNDICQRLVMAR
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 chain8ppv Chain B Residue 1302 [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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PDB8ppv Molecular basis for proof-reading by Family-D DNA polymerases
Resolution3.02 Å
Binding residue
(original residue number in PDB)		C731 C734 C750 C753
Binding residue
(residue number reindexed from 1)		C703 C706 C722 C725
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

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Molecular Function
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Biological Process
External links
PDB RCSB:8ppv, PDBe:8ppv, PDBj:8ppv
PDBsum8ppv
PubMed38097591
UniProtQ9V2F4|DP2L_PYRAB DNA polymerase II large subunit (Gene Name=polC)

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