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(-) Description

Title :  2.45A STRUCTURE OF ETOPOSIDE WITH S.AUREUS DNA GYRASE AND DNA
 
Authors :  B. D. Bax, V. Srikannathasan, P. F. Chan
Date :  04 Jul 15  (Deposition) - 16 Dec 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Type Iia Topoisomerase, Antibacterial, Inhibitor, Isomerase, Fusion Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. F. Chan, V. Srikannathasan, J. Huang, H. Cui, A. P. Fosberry, M. Gu, M. M. Hann, M. Hibbs, P. Homes, K. Ingraham, J. Pizzollo, C. Shen, A. J. Shillings, C. E. Spitzfaden, R. Tanner, A. J. Theobald, R. A. Stavenger, B. D. Bax, M. N. Gwynn
Structural Basis Of Dna Gyrase Inhibition By Antibacterial Qpt-1, Anticancer Drug Etoposide And Moxifloxacin.
Nat Commun V. 6 10048 2015
PubMed-ID: 26640131  |  Reference-DOI: 10.1038/NCOMMS10048
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT A
    Chains: A, C
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 9-491
    Gene: GYRA, SA0006
    Organism Scientific: STAPHYLOCOCCUS AUREUS (STRAIN N315)
    Organism Taxid: 158879
    Strain: N315
 
Molecule 2 - DNA GYRASE SUBUNIT B
    Chains: B, D
    EC Number: 5.99.1.3, 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 417-542, 580-640
    Gene: GYRB, SA0005
    Organism Scientific: STAPHYLOCOCCUS AUREUS (STRAIN N315)
    Organism Taxid: 158879
    Strain: N315
    Synonym: GREEK KEY DELETION CONSTRUCT
 
Molecule 3 - DNA (5'- D(*AP*GP*CP*CP*GP*TP*AP*G*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
    Chains: E, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA (5'- D(*AP*GP*CP*CP*GP*TP*AP*G*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
    Chains: G, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1EVP1Ligand/Ion(5S,5AR,8AR,9R)-9-(4-HYDROXY-3,5-DIMETHOXYPHENYL)-8-OXO-5,5A,6,8,8A,9-HEXAHYDROFURO[3',4':6,7]NAPHTHO[2,3-D][1,3]DIOXOL-5-YL 4,6-O-[(1R)-ETHYLIDENE]-BETA-D-GLUCOPYRANOSIDE
2MN3Ligand/IonMANGANESE (II) ION
3NA2Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:322 , THR A:325 , GLN A:328 , HOH A:899 , HOH A:960binding site for residue NA A 501
2AC2SOFTWAREASP B:508 , ASP B:510 , HOH B:1102 , HOH B:1142 , HOH B:1145 , HOH E:106binding site for residue MN B 1001
3AC3SOFTWAREHOH C:548 , GLU D:435 , ASP D:508 , ASP D:510 , HOH D:802 , HOH D:821 , DG F:8 , HOH H:2202binding site for residue MN D 701
4AC4SOFTWAREHOH A:735 , HOH A:935 , HOH C:754 , DG G:2009 , HOH G:2220binding site for residue MN G 2101
5AC5SOFTWARESER A:84 , GLY B:436 , ASP B:437 , ARG B:458 , GLY B:459 , HOH C:612 , DG E:8 , DG G:2009 , DT G:2010 , DC H:2012 , DC H:2013binding site for residue EVP H 2101
6AC6SOFTWAREHOH F:102 , HOH F:110 , DG H:2009 , HOH H:2204 , HOH H:2206binding site for residue NA H 2102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CDP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CDP)

(-) 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:483
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhhh.........eeee.................eeee..hhhhhhh........eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhh............eee.hhhhhhhhhhheeeeeee.eeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cdp A    9 INERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG  491
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488   


Chain B from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeehhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cdp B  417 KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYA  640
                                   426       436       446       456       466       476       486       496       506       516       526       536       580       590       600       610       620       630       640
                                                                                                                                                          545|                                                            
                                                                                                                                                           580                                                            


Chain C from PDB  Type:PROTEIN  Length:481
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeeehhhhhhhhh........eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhh............eee.hhhhhhhhhhheeeeeee.eeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cdp C   10 NERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQL  490
                                    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       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489 


Chain D from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                              
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.hhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5cdp D  417 KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVY  639
                                   426       436       446       456       466       476       486       496       506       516       526       536       580       590       600       610       620       630         
                                                                                                                                                          545|                                                           
                                                                                                                                                           580                                                           


Chain E from PDB  Type:DNA  Length:8
                                         
                5cdp E    1 AGCCGTAG    8


Chain F from PDB  Type:DNA  Length:8
                                         
                5cdp F    1 AGCCGTAG    8


Chain G from PDB  Type:DNA  Length:12
                                             
                5cdp G 2009 GTACCTACGGCT 2020
                                  2018  


Chain H from PDB  Type:DNA  Length:12
                                             
                5cdp H 2009 GTACCTACGGCT 2020
                                  2018
   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 5CDP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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  5cdp
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  GYRB_STAAN | P66937
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  5.99.1.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        GYRA_STAAN | Q99XG5: 2xco 2xcq 2xcr 2xcs 2xct 4bul 5cdm 5cdn 5cdo 5cdq 5cdr 5iwi 5iwm 5npk 5npp
        GYRB_STAAN | P66937: 2xco 2xcq 2xcr 2xcs 2xct 4bul 5cdm 5cdn 5cdo 5cdq 5cdr 5iwi 5iwm 5npk 5npp

(-) Related Entries Specified in the PDB File

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