Structure of PDB 8ppv Chain B

Receptor sequence
>8ppvB (length=1188) Species: 272844 (Pyrococcus abyssi GE5) [Search protein sequence]
PKEMEEYFEMLQREIDKAYEIAKKARAQGKDPSLDVEIPQATDMAGRVES
LVGPPGVAKRIRELVKEYGKEIAALKIVDEIIEGKFGDLGSREKYAEQAV
RTALAILTEGIVSAPIEGIANVKIKRNTWADNSEYLALYYAGPIRSSGGT
AQALSVLVGDYVRRKLGLDRFKPSEKHIERMVEEVDLYHRAVTRLQYHPS
PEEVRLAMRNIPIEITGEATDDVEVSHRDVPGVETNQLRGGAILVLAEGV
LQKAKKLVKYIDKMGIEGWEWLKEFVEAKEDMGFYYSLYQKFKEEIAPSD
KYAKEVIGGRPLFSDPSKPGGFRLRYGRSRASGFATWGINPATMILVDEF
LAIGTQLKTERPGKGAVVTPVTTIEGPIVKLKDGSVLRVDDYNLALKVRE
DVEEILYLGDAVIAFGDFVENNQTLLPANYCEEWWILEFVKALKEIYEVH
LEPFTENEEESIEEASDYLEIDPEFLKEMLRDPLRVKPPVELAIHFSEVL
GIPLHPYYTLYWNSVEPKDVEKLWRLLKNYAEIEWSNFRGIKFAKKIVIS
QEKLGDSKRTLELLGLPHTVRDGNVIVDYPWAAALLTPLGNLNWEFMAKP
LYATIDIINENNEIKLRDRGISWIGARMGRPEKAKERKMKPPVQVLFPIG
LAGGSSRDIKKAAEEGKVAEVEIAFFKCPKCGHVGPEHLCPNCGTRKELL
WVCPRCNAEYPESQAEGYNYTCPKCNVKLRPYAKRKIRPSELLNRAMENV
KVYGVDKLKGVMGMTSGWKMPEPLEKGLLRAKNDVYVFKDGTIRFDATDA
PITHFRPREIGVSVEKLRELGYTHDFEGKPLVSEDQIVELKPQDIILSKE
AGRYLLKVAKFVDDLLEKFYGLPRFYNAEKMEDLIGHLVIGLAPHTSAGI
VGRIIGFVDALVGYAHPYFHAAKRRNCDGDEDAVMLLLDALLNFSRYYLP
EKRGGKMDAPLVITTRLDPREVDSEVHNMDIVRYYPLEFYEATYELKSPK
ELVGVIERVEDRLGKPEMYYGLKFTHDTDDIALGPKMSLYKQLGDMEEKV
RRQLEVAKRIRAVDEHGVAEKILNSHLIPDLRGNLRSFTRQEFRCVKCNT
KFRRPPLNGKCPVCGGKIVLTVSKGAIEKYLGTAKMLVTEYNVKNYTRQR
ICLTERDIDSLFENVFPETQLTLIVNPNDICQRLVMAR
3D structure
PDB8ppv Molecular basis for proof-reading by Family-D DNA polymerases
ChainB
Resolution3.02 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 P1107 K1129 T1149 P1079 K1101 T1121
BS02 ZN B C706 C718 C678 C690
BS03 ZN B C731 C734 C750 C753 C703 C706 C722 C725
BS04 ZN B C1123 C1139 C1142 C1095 C1111 C1114
BS05 MG B N954 D956 D958 N926 D928 D930
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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