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(-) Description

Title :  BINARY COMPLEX OF 9N DNA POLYMERASE IN THE REPLICATIVE STATE
 
Authors :  K. Betz, K. Diederichs, A. Marx
Date :  19 Apr 13  (Deposition) - 26 Jun 13  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Dna Polymerase, Binary Complex, 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
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: POL, POLA
    Mutation: YES
    Organism Scientific: THERMOCOCCUS
    Organism Taxid: 103799
    Strain: 9ON-7
 
Molecule 2 - DNA (5'- D(P*AP*AP*AP*GP*GP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)-3')
    Chains: T
    Engineered: YES
    Other Details: DNA TEMPLATE
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(DOC))-3')
    Chains: P
    Engineered: YES
    Other Details: DNA PRIMER
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
15CY1Ligand/Ion1-(3-HYDROXYPROPYL)-2-{(1E,3E,5E)-5-[1-(3-HYDROXYPROPYL)-3,3-DIMETHYL-1,3-DIHYDRO-2H-INDOL-2-YLIDENE]PENTA-1,3-DIEN-1-YL}-3,3-DIMETHYL-3H-INDOLIUM
2CL1Ligand/IonCHLORIDE ION
3DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4EDO1Ligand/Ion1,2-ETHANEDIOL
5SO411Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:406 , ARG A:460 , LYS A:487BINDING SITE FOR RESIDUE SO4 A 801
02AC2SOFTWAREARG A:32BINDING SITE FOR RESIDUE SO4 A 802
03AC3SOFTWAREARG A:484 , DA T:1BINDING SITE FOR RESIDUE SO4 A 803
04AC4SOFTWARELYS A:360 , LYS A:363 , ARG A:364 , LEU A:452BINDING SITE FOR RESIDUE SO4 A 804
05AC5SOFTWARETYR A:388 , LYS A:390 , GLU A:391 , HOH A:934BINDING SITE FOR RESIDUE SO4 A 805
06AC6SOFTWAREGLU A:130 , GLY A:131 , ARG A:335 , ARG A:482BINDING SITE FOR RESIDUE SO4 A 806
07AC7SOFTWAREARG A:97 , ASP A:113BINDING SITE FOR RESIDUE SO4 A 807
08AC8SOFTWARETHR A:136 , MET A:137 , ASP A:164 , GLY A:165 , TYR A:320BINDING SITE FOR RESIDUE SO4 A 808
09AC9SOFTWARELYS A:289 , TYR A:291 , ALA A:292BINDING SITE FOR RESIDUE SO4 A 809
10BC1SOFTWARETYR A:110 , PRO A:369 , ASN A:370BINDING SITE FOR RESIDUE CL A 810
11BC2SOFTWAREARG A:406 , SER A:407 , LYS A:487 , HOH A:980 , DA T:2BINDING SITE FOR RESIDUE SO4 A 811
12BC3SOFTWARETYR A:7 , GLN A:91 , PHE A:116 , HOH A:1013BINDING SITE FOR RESIDUE SO4 A 812
13BC4SOFTWAREARG A:99 , ALA A:102 , HIS A:103 , PRO A:104 , ARG A:266 , THR A:267 , ILE A:268 , VAL A:282 , PHE A:283 , GLU A:325 , PHE A:326 , MET A:329 , GLU A:330 , LEU A:333 , THR A:349 , HOH A:1001 , DA T:1 , DA T:2 , DA T:3BINDING SITE FOR RESIDUE 5CY T 101
14BC5SOFTWAREGLY A:245 , DG T:4BINDING SITE FOR RESIDUE EDO T 102

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:428 -A:442
2A:506 -A:509

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:758 -Lys A:759

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K8X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K8X)

(-) Exons   (0, 0)

(no "Exon" information available for 4K8X)

(-) 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:759
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..eeeeeeeeee..eeeeeee.....eeeeee.hhhhhhhhhh.eeee..eeee..eeeeeeeee..eeeeeeeee....hhhhhhhhhhhhh..eeeee....hhhhhhhhhh............eeeeeeee............eeeeeee....eeeee........eee..hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh.............eeeee..eeeee....eeeehhhhhhhhh.....hhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhh.........ee....eeeeeeeeeee.hhhhhhhhhh..............eee......eee....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeee....hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeeee..eeeeee....eeee.hhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhheeee...hhhhh...hhhhhhhhhhhhhh.......eeeeee.....hhhh.eee.hhh.......hhhhhhhhhhhhhhhhhhhhhh..hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k8x A   1 MILDTDYITENGKPVIRVFKKENGEFKIEYDRTFEPYFYALLKDDSAIEDVKKVTAKRHGTVVKVKRAEKVQKKFLGRPIEVWKLYFNHPQDVPAIRDRIRAHPAVVDIYEYDIPFAKRYLIDKGLIPMEGDEELTMLAFAIATLYHEGEEFGTGPILMISYADGSEARVITWKKIDLPYVDVVSTEKEMIKRFLRVVREKDPDVLITYNGDNFDFAYLKKRCEELGIKFTLGRDGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLEAVYEAVFGKPKEKVYAEEIAQAWESGEGLERVARYSMEDAKVTYELGREFFPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAYKRNELAPNKPDERELARRRGGYAGGYVKEPERGLWDNIVYLDFRSLYPSIIITHNVSPDTLNREGCKEYDVAPEVGHKFCKDFPGFIPSLLGDLLEERQKIKRKMKATVDPLEKKLLDYRQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGREYIEMVIRELEEKFGFKVLYADTDGLHATIPGADAETVKKKAKEFLKYINPKLPGLLELEYEGFYVRGFFVTKKKYAVIDEEGKITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIHEQITRDLRDYKATGPHVAVAKRLAARGVKIRPGTVISYIVLKGSGRIGDRAIPADEFDPTKHRYDAEYYIENQVLPAVERILKAFGYRKEDLRYQK 759
                                    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
                                            
                 4k8x P   1 CGCGAACTGCGc  12
                                    10 |
                                      12-DOC


Chain T from PDB  Type:DNA  Length:16
                                                
                 4k8x T   1 AAAGGCGCAGTTCGCG  16
                                    10
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (0, 0)

(no "SCOP Domain" information available for 4K8X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K8X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K8X)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  DPOL_THES9 | Q56366
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  2.7.7.7
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 Related Entries

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        DPOL_THES9 | Q56366: 1qht

(-) Related Entries Specified in the PDB File

1qht APO STRUCTURE OF 9 N DNA POLYMERASE
4k8z