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(-) Description

Title :  BINARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM T. AQUATICUS BOUND TO A PRIMER/TEMPLATE DNA
 
Authors :  Y. Li, G. Waksman
Date :  09 Sep 98  (Deposition) - 13 Jan 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Large Fragement Of Taq Dna Polymerase I, Protein/Dna, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Li, S. Korolev, G. Waksman
Crystal Structures Of Open And Closed Forms Of Binary And Ternary Complexes Of The Large Fragment Of Thermus Aquaticus Dna Polymerase I: Structural Basis For Nucleotide Incorporation.
Embo J. V. 17 7514 1998
PubMed-ID: 9857206  |  Reference-DOI: 10.1093/EMBOJ/17.24.7514
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - PROTEIN (LARGE FRAGMENT OF DNA POLYMERASE I)
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PWB254
    Expression System Strain: X7029
    Expression System Taxid: 562
    Gene: TAQ
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271
    Strain: X7029

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 4KTQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KTQ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:578 -Pro A:579

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KTQ)

(-) 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:539
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4ktqa1 A:294-422 Exonuclease domain of prokaryotic DNA polymerase                                                               d4ktqa2 A:423-832 DNA polymerase I (Klenow fragment)                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 4ktqA01 A:294-446  [code=3.30.420.10, no name defined]                                                                                                   4ktqA02 A:447-563 Taq DNA Polymerase; Chain T, domain 4                                                              4ktqA03 A:564-613,A:758-831                       4ktqA04 A:614-757 5' to 3' exonuclease, C-terminal subdomain                                                                                    4ktqA03 A:564-613,A:758-831  [code=3.30.70.370, no name defined]          - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.........eeee.........eeeeeeee..eeeee..hhhhhh.........hhhhhhhhhhh.........hhhhhhhh......hhhhhhhh...........hhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhh.....................hhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhh..........eee.........eee...........hhhhhhhh.......eeeeeeee..hhhhhhhhhh..hhhhhhhh....hhhh.hhhh...........hhhhhhhhhhhhhh...hhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.eee.....eee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeeeeee...hhhhhhhhhhhhh..........eeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ktq A 294 LEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE 832
                                   303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823         


Chain B from PDB  Type:DNA  Length:12
                                            
                 4ktq B 101 GACCACGGCGCc 112
                                   110 |
                                     112-DOC


Chain C from PDB  Type:DNA  Length:13
                                             
                 4ktq C 204 GGGCGCCGTGGTC 216
                                   213
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:578 - Pro A:579   [ RasMol ]  
 

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  DPO1_THEAQ | P19821
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  2.7.7.7
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 Related Entries

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

UniProtKB/Swiss-Prot
        DPO1_THEAQ | P19821: 1bgx 1jxe 1ktq 1qss 1qsy 1qtm 1taq 1tau 2ktq 3ktq 3lwl 3lwm 3m8r 3m8s 3ojs 3oju 3po4 3po5 3py8 3rr7 3rr8 3rrg 3rrh 3rtv 3sv3 3sv4 3syz 3sz2 3t3f 4bwj 4bwm 4c8k 4c8l 4c8m 4c8n 4c8o 4cch 4df4 4df8 4dfj 4dfk 4dfm 4dfp 4dle 4dlg 4elt 4elu 4elv 4n56 4n5s 4xiu 5e41 5ktq 5nkl 5szt

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4KTQ)