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(-) Description

Title :  2.5A STRUCTURE OF GSK945237 WITH S.AUREUS DNA GYRASE AND 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 :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
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
    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 409-543, 580-644,UNP RESIDUES 409-543, 580- 644
    Gene: GYRB, SA0005
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 158879
    Strain: N315
 
Molecule 2 - DNA GYRASE SUBUNIT A
    Chains: A, C
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GYRA, SA0006
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
 
Molecule 3 - DNA (5'- D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*TP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA (5'- D(*TP*GP*TP*GP*CP*GP*GP*TP*GP*AP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
    Chains: F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
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
2GOL1Ligand/IonGLYCEROL
3MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:435 , ASP B:508 , HOH B:803 , HOH B:814 , DG E:8 , DG E:9 , DT F:8 , DG F:9binding site for residue MN B 701
2AC2SOFTWAREGLU D:435 , ASP D:508 , HOH D:1106 , HOH D:1121 , DG E:8 , DG E:9 , DT F:8 , DG F:9binding site for residue MN D 1001
3AC3SOFTWAREPRO C:44 , ARG C:47 , ARG C:48 , GLU C:156 , HOH C:647binding site for residue GOL C 501
4AC4SOFTWAREALA 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 , DT E:11 , DA F:10 , DA F:11 , HOH F:212 , HOH F:219binding site for residue 6EJ F 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:490 -Gly A:491
2Gly C:253 -Gly C:254

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IWM)

(-) 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 ..eeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhhh.........eeee.................eeee...hhhhhh........eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhh....hhhhhh............eee.hhhhhhhhhhheeeeeee.eeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iwm 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:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.hhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iwm B 417 KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVY 639
                                   426       436       446       456       466       476       486       496       506       516       526       536       580       590       600       610       620       630         
                                                                                                                                                          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...hhhhhhhhhhhh..........eeee.................eeee..hhhhhhh........eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhh............eee.hhhhhhhhhhheeeeeee.eeeeee.....eeeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iwm 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...eeee....hhhhhhhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iwm 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
                                                    
                 5iwm E   1 AGCCGTAGGTTCACCGCACA  20
                                    10        20


Chain F from PDB  Type:DNA  Length:20
                                                    
                 5iwm F   1 TGTGCGGTGAACCTACGGCT  20
                                    10        20
   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 5IWM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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  GYRA_STAAN | Q99XG5
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  GYRB_STAAN | P66937
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  GYRB_STAAU | P0A0K8
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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 5cdp 5cdq 5cdr 5iwi 5npk 5npp
        GYRB_STAAN | P66937: 2xco 2xcq 2xcr 2xcs 2xct 4bul 5cdm 5cdn 5cdo 5cdp 5cdq 5cdr 5iwi 5npk 5npp
        GYRB_STAAU | P0A0K8: 3g75 3g7b 3ttz 3u2d 3u2k 4plb 4urm 4uro 5bs3 5cph 5ctu 5ctw 5ctx 5cty 5d6p 5d6q 5d7c 5d7d 5d7r 5iwi

(-) Related Entries Specified in the PDB File

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