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(-) Description

Title :  POYMERASE NUCLEOTIDE COMPLEX
 
Authors :  D. T. Nair, J. Kottur
Date :  20 Jun 15  (Deposition) - 22 Jun 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,F,G,H
Biol. Unit 1:  F,G,H  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Dna Polymerase, Replication, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kottur, D. T. Nair
Reactive Oxygen Species Play An Important Role In The Bactericidal Activity Of Quinolone Antibiotics
Angew. Chem. Int. Ed. Engl. V. 55 2397 2016
PubMed-ID: 26757158  |  Reference-DOI: 10.1002/ANIE.201509340

(-) Compounds

Molecule 1 - DNA POLYMERASE IV
    Chains: F, A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P1
    Expression System Strain: C41DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DINB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: [NUMBER SIGN]1/H766
    Synonym: POL IV
 
Molecule 2 - DNA (5'- D(*TP*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
    Chains: G, H, B, C
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCFGH
Biological Unit 1 (1x):    FGH
Biological Unit 2 (1x): ABC   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
18GT1Ligand/Ion8-OXO-GUANOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
18GT-1Ligand/Ion8-OXO-GUANOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
18GT1Ligand/Ion8-OXO-GUANOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , MET A:9 , ASP A:10 , CYS A:11 , PHE A:12 , PHE A:13 , SER A:42 , THR A:43 , ARG A:49 , SER A:55 , ASP A:103 , GLU A:104 , LYS A:157 , MG A:402 , HOH A:507 , HOH A:520 , DA B:840 , DG B:841 , DC C:873binding site for residue 8GT A 401
2AC2SOFTWAREASP A:8 , MET A:9 , ASP A:103 , 8GT A:401binding site for residue MG A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C5J)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys F:157 -Pro F:158
2Lys A:157 -Pro A:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C5J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C5J)

(-) Exons   (0, 0)

(no "Exon" information available for 5C5J)

(-) Sequences/Alignments

Asymmetric 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:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.hhhhhhhhhhhhhhh...eeee........eeeehhhhhh.......hhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhh..eeeee..eeeee.........hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh....eee.hhhhhhhhhhh.hhhhh...hhhhhhhhhhh...hhhhhhh.hhhhhhhhhhhhhhhhhhhh...............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee....eeeeeee....hhhhhhhhhhhhhhhhh....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5c5j A   0 GSRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRTCGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDP 341
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  


Chain B from PDB  Type:DNA  Length:18
                                                  
                 5c5j B 837 TCTAGGGTCCTAGGACCC 854
                                   846        


Chain C from PDB  Type:DNA  Length:17
                                                 
                 5c5j C 857 CTAGGGTCCTAGGACCC 873
                                   866       


Chain F from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.hhhhhhhhhhhhhhh...eeee........eeeehhhhhhh......hhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh....eeeee..eeeee.........hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh......eee....hhhhhhhh.hhhhh...hhhhhhhhhh....hhhhhhh.hhhhhhhhhhhhhhhhhhhh...............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeee....eeeeeee....hhhhhhhhhhhhhhhhh....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5c5j F   0 GSRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRTCGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDP 341
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  


Chain G from PDB  Type:DNA  Length:18
                                                  
                 5c5j G 837 TCTAGGGTCCTAGGACCC 854
                                   846        


Chain H from PDB  Type:DNA  Length:14
                                              
                 5c5j H 860 GGGTCCTAGGACCC 873
                                   869
   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 5C5J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C5J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C5J)

(-) Gene Ontology  (17, 29)

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 Related Entries

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UniProtKB/Swiss-Prot
        DPO4_ECOLI | Q47155: 1ok7 1unn 4ir1 4ir9 4irc 4ird 4irk 4q43 4q44 4q45 4r8u

(-) Related Entries Specified in the PDB File

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