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An Information Portal to 105097 Biological Macromolecular Structures

KOD Polymerase in binary complex with dsDNA
Biology and Chemistry Report
4K8Z
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE/DNA
    Text DNA Polymerase, TRANSFERASE-DNA complex

    Polymeric Molecules

    Chain A
    Description DNA polymerase 
    Mutation D141A, E143A 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 90061.1 
    Source Method genetically manipulated  
    Chain T
    Description DNA (5'-D(*AP*AP*AP*TP*TP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 4898.2 
    Source Method synthetic  
    Chain P
    Description DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(2DA))-3') 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polydeoxyribonucleotide 
    Formula Weight 3656.4 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    EDO  1,2-ETHANEDIOL  C2 H6 O2   62.07  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    NCO  COBALT HEXAMMINE(III)  Co H18 N6   161.12  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A D0VWU9_THEKO D0VWU9     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    2.7.7.7      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6139   Nucleobase Containing Compound Metabolic Process  Any Cellular Metabolic Process Involving Nucleobases Nucleosides Nucleotides and Nucleic Acids. 
    6260   DNA Replication  The Cellular Metabolic Process in Which a Cell Duplicates One or More Molecules of Dna. DNA Replication Begins When Specific Sequences Known As Origins of Replication Are Recognized and Bound by Initiation Proteins and Ends When the Original DNA Molecule Has Been Completely Duplicated and the Copies Topologically Separated. the Unit of Replication Usually Corresponds to the Genome of the Cell an Organelle or a Virus. the Template For Replication Can Either Be an Existing DNA Molecule or Rna. 
    71897   DNA Biosynthetic Process  The Cellular DNA Metabolic Process Resulting in the Formation of DNA Deoxyribonucleic Acid One of the Two Main Types of Nucleic Acid Consisting of a Long Unbranched Macromolecule Formed From One or Two Strands of Linked Deoxyribonucleotides the 3' Phosphate Group of Each Constituent Deoxyribonucleotide Being Joined in 3' 5' Phosphodiester Linkage to the 5' Hydroxyl Group of the Deoxyribose Moiety of the Next One. 
    166   Nucleotide Binding  Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 
    3676   Nucleic Acid Binding  Interacting Selectively and Non Covalently with Any Nucleic Acid. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    3887   DNA Directed DNA Polymerase Activity  Catalysis of the Reaction: Deoxynucleoside Triphosphate + Dna(n) = Diphosphate + Dna(n+1); the Synthesis of DNA From Deoxyribonucleotide Triphosphates in the Presence of a DNA Template and a 3'hydroxyl Group. 
    16740   Transferase Activity  Catalysis of the Transfer of a Group E.g. a Methyl Group Glycosyl Group Acyl Group Phosphorus Containing or Other Groups From One Compound (generally Regarded As the Donor) to Another Compound (generally Regarded As the Acceptor). Transferase Is the Systematic Name For Any Enzyme of EC Class 2. 
    16779   Nucleotidyltransferase Activity  Catalysis of the Transfer of a Nucleotidyl Group to a Reactant. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Scientific Name Thermococcus kodakarensis  
    Strain KOD1
    Gene pol, pol tk0001, tk0001
    Host Scientific Name Escherichia coli  
    Host Strain Bl21 De3
    Host Vector Type Plasmid
    Host Plasmid Name pET24a


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    - - 3233723     DNA-dependent DNA polymerase family B protein TK0001