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(-) Description

Title :  1.98A STRUCTURE OF GSK945237 WITH S.AUREUS DNA GYRASE AND SINGLY NICKED DNA
 
Authors :  B. D. Bax, T. J. Miles
Date :  22 Mar 16  (Deposition) - 25 May 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G
Keywords :  Type Iia Topoisomerase, Antibacterial, Inhibitor, Isomerase, Fusion Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. J. Miles, A. J. Hennessy, B. Bax, G. Brooks, B. S. Brown, P. Brown, N. Cailleau, D. Chen, S. Dabbs, D. T. Davies, J. M. Esken, I. Giordano, J. L. Hoover, G. E. Jones, S. K. Kusalakumari Sukmar, R. E. Markwell, E. A. Minthorn, S. Rittenhouse, M. N. Gwynn, N. D. Pearson
Novel Tricyclics (E. G. , Gsk945237) As Potent Inhibitors Of Bacterial Type Iia Topoisomerases.
Bioorg. Med. Chem. Lett. V. 26 2464 2016
PubMed-ID: 27055939  |  Reference-DOI: 10.1016/J.BMCL.2016.03.106

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT B,DNA GYRASE SUBUNIT B
    ChainsB, D
    EC Number5.99.1.3, 5.99.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneGYRB, SA0005
    Organism ScientificSTAPHYLOCOCCUS AUREUS
    Organism Taxid1280
 
Molecule 2 - DNA GYRASE SUBUNIT A
    ChainsA, C
    EC Number5.99.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneGYRA, SA0006
    Organism ScientificSTAPHYLOCOCCUS AUREUS (STRAIN N315)
    Organism Taxid158879
    StrainN315
 
Molecule 3 - DNA (5'- D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3')
    ChainsE
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    Other DetailsCHAIN E WAS A 20MER. CHAIN F WAS AN 8MER TGTGCGGT AND A 12MER GTACCTACGGCT. NOTE THE 20MER, 8MER AND 12MER WERE ANNEALED TOGETHER TO GIVE A NICKED DNA DUPLEX. THIS DISPLAYED STATIC DISORDER AROUND THE NON-CRYSTALLOGRAPHIC TWOFOLD AXIS.
    SyntheticYES
 
Molecule 4 - DNA (5'- D(*TP*GP*TP*GP*CP*GP*GP*T*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
    ChainsF
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    Other DetailsCHAIN F WAS AN 8MER TGTGCGGT AND A 12MER GTACCTACGGCT . COULD BE DESCRIBED AS TWO SEPARATE CHAINS. NOTE CHAIN E WAS A 20MER. THE 20MER, 8MER AND 12MER WERE ANNEALED TOGETHER TO GIVE A NICKED DNA DUPLEX. THIS DISPLAYED STATIC DISORDER AROUND THE NC TWOFOLD AXIS.
    SyntheticYES
 
Molecule 5 - DNA (5'- D(*TP*GP*TP*GP*CP*GP*GP*T*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
    ChainsG
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    Other DetailsCHAIN F WAS AN 8MER TGTGCGGT AND A 12MER GTACCTACGGCT . COULD BE DESCRIBED AS TWO SEPARATE CHAINS. NOTE CHAIN E WAS A 20MER. THE 20MER, 8MER AND 12MER WERE ANNEALED TOGETHER TO GIVE A NICKED DNA DUPLEX. THIS DISPLAYED STATIC DISORDER AROUND THE NC TWOFOLD AXIS.
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234567
Asymmetric/Biological Unit ABCDEFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
16EJ1Ligand/Ion(1R)-1-[(4-{[(6,7-DIHYDRO[1,4]DIOXINO[2,3-C]PYRIDAZIN-3-YL)METHYL]AMINO}PIPERIDIN-1-YL)METHYL]-9-FLUORO-1,2-DIHYDRO-4H-PYRROLO[3,2,1-IJ]QUINOLIN-4-ONE
2CL1Ligand/IonCHLORIDE ION
3GOL10Ligand/IonGLYCEROL
4MN3Ligand/IonMANGANESE (II) ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU B:435 , ASP B:508 , ASP B:510 , LYS B:581 , HOH B:802 , HOH B:809 , HOH B:821 , DG E:8 , DG E:9 , DT F:1008binding site for residue MN B 701
02AC2SOFTWAREPHE A:97 , SER A:112 , GLY A:115 , GLN A:267 , HOH A:715 , HOH A:812 , DC E:4 , DG F:1004binding site for residue GOL A 501
03AC3SOFTWAREARG A:47 , ARG A:48 , PRO A:157 , HOH A:627 , HOH A:651 , HOH A:671 , HOH A:798binding site for residue GOL A 502
04AC4SOFTWAREASP A:96 , PRO A:219 , ARG A:485 , HOH A:660binding site for residue GOL A 503
05AC5SOFTWAREGLU A:250 , THR A:262 , ARG A:303 , HOH A:628 , HOH A:635binding site for residue GOL A 504
06AC6SOFTWAREASN A:54 , GLU A:55 , ASN A:140binding site for residue GOL A 505
07AC7SOFTWAREASN A:313 , HOH A:728 , GLN C:257 , ASP C:311 , ALA C:312 , GOL C:503 , HOH C:746binding site for residue GOL A 506
08AC8SOFTWARESER A:315 , HOH A:729 , SER C:315binding site for residue CL A 507
09AC9SOFTWAREGLU D:435 , ASP D:508 , ASP D:510 , LYS D:581 , HOH D:1101 , HOH D:1126 , HOH D:1148 , DG E:8 , DG E:9 , DT F:1008binding site for residue MN D 1001
10AD1SOFTWAREHIS C:390 , HOH C:706 , HOH C:901 , DT F:1001 , HOH F:1106binding site for residue MN C 501
11AD2SOFTWAREPRO C:44 , ARG C:47 , GLU C:156 , HOH C:606 , HOH C:648 , HOH C:654binding site for residue GOL C 502
12AD3SOFTWAREARG A:244 , ASN A:319 , GOL A:506 , GLU C:251 , GLY C:255 , ARG C:256 , GLN C:257 , HOH C:602 , HOH C:603 , HOH C:728binding site for residue GOL C 503
13AD4SOFTWAREASP B:470 , ARG C:385 , HOH C:617binding site for residue GOL C 504
14AD5SOFTWAREMET C:113 , GLN C:267 , HOH C:605 , HOH C:750 , HOH C:801 , DG F:1004binding site for residue GOL C 505
15AD6SOFTWAREALA A:68 , MET A:75 , ASP A:83 , MET A:121 , ALA C:68 , MET C:75 , ASP C:83 , MET C:121 , DT E:10 , DA E:11 , HOH E:202 , HOH E:203 , HOH E:222 , HOH E:237 , DT G:2010 , DA G:2011binding site for residue 6EJ E 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:490 -Gly A:491

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IWI)

(-) 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.................eeeehhhhhhhhh........eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhhhhh.........eee.hhhhhhhhhhheeeeeee.eeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5iwi 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:192
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhh.eeeee.hhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5iwi B  415 PGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYA  640
                                   424       434       444       454       464       474       484       494       504       514       524       534       544||     588       598       608       618       628       638  
                                                                                                                                                            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 .eeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhhh.........eeee.................eeeehhhhhhhhh........eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhh....hhhhhh............eee.hhhhhhhhhhheeeeeee.eeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5iwi 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 .............eeeeeehhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5iwi 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:20
                                                     
                5iwi E    1 AGCCGTAGGTACACCGCACA   20
                                    10        20

Chain F from PDB  Type:DNA  Length:8
                                         
                5iwi F 1001 TGTGCGGT 1008

Chain G from PDB  Type:DNA  Length:12
                                             
                5iwi G 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 5IWI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 37)

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
        GYRA_STAAN | Q99XG52xco 2xcq 2xcr 2xcs 2xct 4bul 5cdm 5cdn 5cdo 5cdp 5cdq 5cdr 5iwm 5npk 5npp
        GYRB_STAAN | P669372xco 2xcq 2xcr 2xcs 2xct 4bul 5cdm 5cdn 5cdo 5cdp 5cdq 5cdr 5iwm 5npk 5npp
        GYRB_STAAU | P0A0K83g75 3g7b 3ttz 3u2d 3u2k 4plb 4urm 4uro 5bs3 5cph 5ctu 5ctw 5ctx 5cty 5d6p 5d6q 5d7c 5d7d 5d7r 5iwm

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5IWI)