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FASTA Sequence PDB Format mmCIF Format
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8PPV

Intermediate conformer of pyrococcus abyssi dna polymerase d (pold) bound to a primer/template substrate containing three consecutive mismatches

PDB DOI: 10.2210/pdb8ppv/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Pyrococcus Abyssi Ge5 , Synthetic Construct

Deposited: 2023-07-10
Deposition Author(s): Betancurt-Anzola, L. , Gardner, A.F. , Martinez-Carranza, M. , Sauguet, L. , Zatopek, K.M.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.02 Å

8ppv
Literature

Intermediate conformer of pyrococcus abyssi dna polymerase d (pold) bound to a primer/template substrate containing three consecutive mismatches

Betancurt-Anzola, L. , Gardner, A.F. , Martinez-Carranza, M. , Sauguet, L. , Zatopek, K.M.

Primary Citation of Related Structures: 8PPV


Proteins
Molecule Chains Sequence Length Organism Sequence
DNA polymerase II small subunit A 662 Pyrococcus Abyssi Ge5 , Synthetic Construct MGKHHHHSGHHHTGHHHHSGSHHHTSSSASTGENLYFQGTGDGSDELVKALERAGYLLTPSAYYLLVDHFKEGKFSLVELVKFAKSKGVFIIDGDLAYEFLQFLGLGVPQEIKESYISTGEEAEKTVESQETRASELEEGGVSQVSSGELQELKEESPEISTTEEEIGGLELVQSSISTGSEVEYNNGENGESVVVLDKYGYPILYAPEEIGEEKEYSKYEDVVIEWNPSVTPVQIEKNYEVKFDVRQVKLRPPKVKNGSGKEGEIIVEAYASLFKSRLSKLKRILRENPEISNVVDIGKLNYVSGDEEVTIIGLVNSKRETNRGLIFEVEDKTGIVKVFLPKDSEDYREAFKVLPDAVVAFKGFYSKKGIFFANKFYLPDVPLYRKQKPPLEEKVYAILISDIHVGSREFCEKAFLKFLEWLNGHVESKEEEEIVSRVKYLIIAGDVVDGIGIYPGQYSDLVIPDIFDQYEALANLLANVPEHITMFIGPGNADAARPAIPQPEFYKEYAKPIYKLKNAIIISNPAVIRLHGRDFLIAHGRGIEDVVSFVPGLTHHKPGLPMVELLKMRHLAPTFGGKVPIAPDPEDLLVIEEVPDLVQMGHVHVYDAVVYRGVQLVNSATWQAQTEFQKMVNIVPTPAKVPVVDVESARVVKVLDFSGWC
DP2 B 1270 Pyrococcus Abyssi Ge5 , Synthetic Construct MELPKEMEEYFEMLQREIDKAYEIAKKARAQGKDPSLDVEIPQATDMAGRVESLVGPPGVAKRIRELVKEYGKEIAALKIVDEIIEGKFGDLGSREKYAEQAVRTALAILTEGIVSAPIEGIANVKIKRNTWADNSEYLALYYAGPIRSSGGTAQALSVLVGDYVRRKLGLDRFKPSEKHIERMVEEVDLYHRAVTRLQYHPSPEEVRLAMRNIPIEITGEATDDVEVSHRDVPGVETNQLRGGAILVLAEGVLQKAKKLVKYIDKMGIEGWEWLKEFVEAKEKGEPKEEGKEESLAESTLEETKVEVDMGFYYSLYQKFKEEIAPSDKYAKEVIGGRPLFSDPSKPGGFRLRYGRSRASGFATWGINPATMILVDEFLAIGTQLKTERPGKGAVVTPVTTIEGPIVKLKDGSVLRVDDYNLALKVREDVEEILYLGDAVIAFGDFVENNQTLLPANYCEEWWILEFVKALKEIYEVHLEPFTENEEESIEEASDYLEIDPEFLKEMLRDPLRVKPPVELAIHFSEVLGIPLHPYYTLYWNSVEPKDVEKLWRLLKNYAEIEWSNFRGIKFAKKIVISQEKLGDSKRTLELLGLPHTVRDGNVIVDYPWAAALLTPLGNLNWEFMAKPLYATIDIINENNEIKLRDRGISWIGARMGRPEKAKERKMKPPVQVLFPIGLAGGSSRDIKKAAEEGKVAEVEIAFFKCPKCGHVGPEHLCPNCGTRKELLWVCPRCNAEYPESQAEGYNYTCPKCNVKLRPYAKRKIRPSELLNRAMENVKVYGVDKLKGVMGMTSGWKMPEPLEKGLLRAKNDVYVFKDGTIRFDATDAPITHFRPREIGVSVEKLRELGYTHDFEGKPLVSEDQIVELKPQDIILSKEAGRYLLKVAKFVDDLLEKFYGLPRFYNAEKMEDLIGHLVIGLAPHTSAGIVGRIIGFVDALVGYAHPYFHAAKRRNCDGDEDAVMLLLDALLNFSRYYLPEKRGGKMDAPLVITTRLDPREVDSEVHNMDIVRYYPLEFYEATYELKSPKELVGVIERVEDRLGKPEMYYGLKFTHDTDDIALGPKMSLYKQLGDMEEKVRRQLEVAKRIRAVDEHGVAEKILNSHLIPDLRGNLRSFTRQEFRCVKCNTKFRRPPLNGKCPVCGGKIVLTVSKGAIEKYLGTAKMLVTEYNVKNYTRQRICLTERDIDSLFENVFPETQLTLIVNPNDICQRLVMARTGEVNKSGLLENLSNGSKKTEKAEKAEKPRKKSDEKPKKKRVISLEEFFSRKSK
DNA polymerase sliding clamp C 261 Pyrococcus Abyssi Ge5 , Synthetic Construct MRGSHHHHHHGSMPFEIVFEGAKEFAQLIETASRLIDEAAFKVTEEGISMRAMDPSRVVLIDLNLPASIFSKYEVDGEETIGVNMDHLKKVLKRGKAKETLILRKGEENFLEISLQGTATRTFKLPLIDVEEIEVDLPELPFTAKVVILGDVIKEAVKDASLVSDSMKFIAKENEFTMRAEGETQEVEVKLTLEDEGLLDIEVQEETKSAYGISYLSDMVKGLGKADEVTIKFGNEMPMQMEYYIRDEGRLIFLLAPRVEE
DNA polymerase sliding clamp D 261 Pyrococcus Abyssi Ge5 , Synthetic Construct MRGSHHHHHHGSMPFEIVFEGAKEFAQLIETASRLIDEAAFKVTEEGISMRAMDPSRVVLIDLNLPASIFSKYEVDGEETIGVNMDHLKKVLKRGKAKETLILRKGEENFLEISLQGTATRTFKLPLIDVEEIEVDLPELPFTAKVVILGDVIKEAVKDASLVSDSMKFIAKENEFTMRAEGETQEVEVKLTLEDEGLLDIEVQEETKSAYGISYLSDMVKGLGKADEVTIKFGNEMPMQMEYYIRDEGRLIFLLAPRVEE
DNA polymerase sliding clamp E 261 Pyrococcus Abyssi Ge5 , Synthetic Construct MRGSHHHHHHGSMPFEIVFEGAKEFAQLIETASRLIDEAAFKVTEEGISMRAMDPSRVVLIDLNLPASIFSKYEVDGEETIGVNMDHLKKVLKRGKAKETLILRKGEENFLEISLQGTATRTFKLPLIDVEEIEVDLPELPFTAKVVILGDVIKEAVKDASLVSDSMKFIAKENEFTMRAEGETQEVEVKLTLEDEGLLDIEVQEETKSAYGISYLSDMVKGLGKADEVTIKFGNEMPMQMEYYIRDEGRLIFLLAPRVEE

Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
DNA (5'-D(*P*CP*CP*GP*GP*GP*CP*CP*GP*AP*GP*CP*CP*GP*TP*(GS)P*(G7P)P*(PST)P*(PST)P*(PST))-3') p 21 NA CGCCGGGCCGAGCCGTGXTTT
DNA (5'-D(P*AP*GP*CP*AP*CP*GP*GP*CP*TP*CP*GP*GP*CP*CP*CP*GP*G)-3') t 25 NA AGGTCGTGCACGGCTCGGCCCGGCG
Experimental Data

Method: ELECTRON MICROSCOPY

Deposited Date: 2023-07-10
Deposition Author(s): Betancurt-Anzola, L. , Gardner, A.F. , Martinez-Carranza, M. , Sauguet, L. , Zatopek, K.M.