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(-) Description

Title :  KOD POLYMERASE IN BINARY COMPLEX WITH DSDNA
 
Authors :  K. Bergen, K. Betz, W. Welte, K. Diederichs, A. Marx
Date :  19 Apr 13  (Deposition) - 26 Jun 13  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Dna Polymerase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Bergen, K. Betz, W. Welte, K. Diederichs, A. Marx
Structures Of Kod And 9N Dna Polymerases Complexed With Primer Template Duplex
Chembiochem V. 14 1058 2013
PubMed-ID: 23733496  |  Reference-DOI: 10.1002/CBIC.201300175

(-) Compounds

Molecule 1 - DNA POLYMERASE
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24A
    Expression System StrainBL21-DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePOL, POL TK0001, TK0001
    MutationYES
    Organism ScientificTHERMOCOCCUS KODAKARENSIS
    Organism Taxid69014
    StrainKOD1
 
Molecule 2 - DNA (5'-D(*AP*AP*AP*TP*TP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)- 3')
    ChainsT
    EngineeredYES
    Other DetailsDNA PRIMER
    SyntheticYES
 
Molecule 3 - DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(2DA))-3')
    ChainsP
    EngineeredYES
    Other DetailsDNA TEMPLATE
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
12DA1Mod. Nucleotide2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MG1Ligand/IonMAGNESIUM ION
4NCO1Ligand/IonCOBALT HEXAMMINE(III)

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:568 , LEU A:571 , GLY A:573 , LEU A:575 , GLU A:576BINDING SITE FOR RESIDUE NCO A 801
2AC2SOFTWAREGLY A:167 , ALA A:168 , TYR A:180 , LYS A:317BINDING SITE FOR RESIDUE EDO A 802
3AC3SOFTWAREASN A:210 , HOH A:1005BINDING SITE FOR RESIDUE EDO A 803
4AC4SOFTWAREDG T:7 , DC T:8BINDING SITE FOR RESIDUE MG T 101

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:428 -A:442

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K8Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K8Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K8Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4K8Z)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:756
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4k8za1 A:1-347 automated matches                                                                                                                                                                                                                                                                                                                          d4k8za2 A:348-756 automated matches                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee..eeeeeeeeee..eeeeeee.....eeeeee.hhhhhhhhhh..ee....ee...eeeeeeeee..eeeeeeeee....hhhhhhhhhhhh...eeeee....hhhhhhhhhh............eeeeeeee............eeeeeeee..eeeeee........eee..hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh............eeeee..eeeee....eeeehhhhhhhhh.....hhhhhhhhhh.......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhh..............eeeeeeeeeee.hhhhhhhhhh..............eee......eee....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...eeeee....hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeeee..eeeee.....eeee.hhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhheeee...hhhhh...hhhhhhhhhhhhh........eeeeee.....hhhh.eee.hhh.......hhhhhhhhhhhhhhhhhhhhhh.hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k8z A   1 MILDTDYITEDGKPVIRIFKKENGEFKIEYDRTFEPYFYALLKDDSAIEEVKKITAERHGTVVTVKRVEKVQKKFLGRPVEVWKLYFTHPQDVPAIRDKIREHPAVIDIYEYDIPFAKRYLIDKGLVPMEGDEELKMLAFAIATLYHEGEEFAEGPILMISYADEEGARVITWKNVDLPYVDVVSTEREMIKRFLRVVKEKDPDVLITYNGDNFDFAYLKKRCEKLGINFALGRDGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGQPKEKVYAEEITTAWETGENLERVARYSMEDAKVTYELGKEFLPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAYERNELAPNKPDEKELARRRQSYEGGYVKEPERGLWENIVYLDFRSLYPSIIITHNVSPDTLNREGCKEYDVAPQVGHRFCKDFPGFIPSLLGDLLEERQKIKKKMKATIDPIERKLLDYRQRAIKILANSYYGYYGYARARWYCKECAESVTAWGREYITMTIKEIEEKYGFKVIYSDTDGFFATIPGADAETVKKKAMEFLKYINAKLPGALELEYEGFYKRGFFVTKKKYAVIDEEGKITTRGLEIVRRDWSEIAKETQARVLEALLKDGDVEKAVRIVKEVTEKLSKYEVPPEKLVIHEQITRDLKDYKATGPHVAVAKRLAARGVKIRPGTVISYIVLKGSGRIGDRAIPFDEFDPTKHKYDAEYYIENQVLPAVERILRAFGYRKEDLR 756
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750      

Chain P from PDB  Type:DNA  Length:12
                                            
                 4k8z P   1 CGCGAACTGCGx  12
                                    10 |
                                      12-2DA

Chain T from PDB  Type:DNA  Length:14
                                              
                 4k8z T   3 ATTCGCAGTTCGCG  16
                                    12    

   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K8Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K8Z)

(-) Gene Ontology  (15, 25)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DPOL_THEKO | P779331wn7 1wns 2cw7 2cw8
UniProtKB/TrEMBL
        D0VWU9_THEKO | D0VWU91wn7

(-) Related Entries Specified in the PDB File

1qht 1wns 4k8x