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(-) Description

Title :  2.22A STRUCTURE OF THIOPHENE2 AND GSK945237 WITH S.AUREUS DNA GYRASE AND DNA
 
Authors :  B. D. Bax, P. F. Chan, R. A. Stavenger
Date :  18 Apr 17  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Type Iia Topoisomerase, Antibacterial, Inhibitor, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. F. Chan, T. Germe, B. D. Bax, J. Huang, R. K. Thalji, E. Bacque, A. Checchia, D. Chen, H. Cui, X. Ding, K. Ingraham, L. Mccloskey, K. Raha, V. Srikannathasan, A. Maxwell, R. A. Stavenger
Thiophene Antibacterials That Allosterically Stabilize Dna-Cleavage Complexes With Dna Gyrase.
Proc. Natl. Acad. Sci. V. 114 E4492 2017 U. S. A.
PubMed-ID: 28507124  |  Reference-DOI: 10.1073/PNAS.1700721114

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT B,DNA GYRASE SUBUNIT B,DNA GYRASE SUBUNIT A
    Chains: B, D
    EC Number: 5.99.1.3, 5.99.1.3, 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GYRB, SA0005, GYRA, SA0006
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 158879
    Strain: N315
 
Molecule 2 - DNA (5'- D(*AP*GP*CP*CP*GP*TP*AP*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 3 - DNA (5'- D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
    Chains: A, C
    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  (6, 16)

Asymmetric/Biological Unit (6, 16)
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
294K2Ligand/Ion~{N}-[(1~{R})-2-AZANYL-1-PHENYL-ETHYL]-5-(2-CHLOROPHENYL)-2-METHYL-THIOPHENE-3-CARBOXAMIDE
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4GOL9Ligand/IonGLYCEROL
5MN2Ligand/IonMANGANESE (II) ION
6NA1Ligand/IonSODIUM ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP B:508 , ASP B:510 , HOH B:1740 , HOH B:1765 , HOH B:1796 , HOH D:1714binding site for residue MN B 1501
02AC2SOFTWAREARG B:630 , ILE B:633 , GLU B:634 , VAL B:1031 , MET B:1179 , ARG B:1342 , PRO B:1343 , HOH B:1826 , HOH B:1833binding site for residue 94K B 1502
03AC3SOFTWAREGLU B:1251 , GLY B:1255 , ARG B:1256 , HOH B:1605 , HOH B:1861 , SER D:1315 , ASN D:1319binding site for residue GOL B 1503
04AC4SOFTWAREARG B:1047 , ARG B:1048 , ILE B:1147 , GLU B:1156 , HOH B:1673 , HOH B:1722 , HOH B:1746binding site for residue GOL B 1504
05AC5SOFTWAREGLU B:1190 , GLU B:1214 , ASP B:1482 , ASP B:1483 , ARG B:1484 , HOH B:1721binding site for residue GOL B 1505
06AC6SOFTWARETYR B:1322 , LYS B:1323 , THR B:1325 , GLN B:1328 , HOH B:1926 , HOH D:1916binding site for residue NA B 1506
07AC7SOFTWAREPHE B:1097 , MET B:1113 , GLY B:1115 , HOH B:1904 , HOH B:1963binding site for residue DMS B 1507
08AC8SOFTWAREASP D:508 , ASP D:510 , HOH D:1673 , HOH D:1683 , HOH D:1738 , HOH F:112binding site for residue MN D 1501
09AC9SOFTWAREARG D:630 , ILE D:633 , GLU D:634 , ALA D:637 , VAL D:1031 , MET D:1179 , ARG D:1342 , PRO D:1343 , HOH D:1672 , HOH D:1828 , HOH D:1899 , HOH D:1965binding site for residue 94K D 1502
10AD1SOFTWAREPRO D:1044 , ARG D:1047 , GLU D:1156 , HOH D:1688 , HOH D:1737 , HOH D:1837binding site for residue GOL D 1503
11AD2SOFTWAREARG B:1244 , ASN B:1319 , GLU D:1251 , GLY D:1255 , ARG D:1256 , GLN D:1257 , HOH D:1678 , HOH D:1754binding site for residue GOL D 1504
12AD3SOFTWAREGLY D:1115 , GLN D:1267 , HOH D:1818 , HOH D:1866 , DC F:-5binding site for residue GOL D 1505
13AD4SOFTWAREASP D:1389 , HIS D:1390 , DA E:-8binding site for residue GOL D 1506
14AD5SOFTWAREDG A:1 , DT A:2 , HOH A:216 , SER B:1084 , HOH B:1742 , DG E:-1binding site for residue GOL A 101
15AD6SOFTWAREDT A:2 , DA A:3 , ALA B:1068 , GLY B:1072 , MET B:1075 , ASP B:1083 , MET B:1121 , HOH B:1727 , HOH B:1855 , DT C:2 , DA C:3 , HOH C:219 , ALA D:1068 , MET D:1075 , ASP D:1083 , MET D:1121binding site for residue 6EJ C 101
16AD7SOFTWAREDG C:1 , DT C:2 , HOH C:206 , HOH C:208 , SER D:1084 , HOH D:1669 , DA F:-2 , DG F:-1binding site for residue GOL C 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu B:1490 -Gly B:1491

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5NPP)

(-) 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:DNA  Length:12
                                             
                5npp A    1 GTACCTACGGCT   12
                                    10  


Chain B from PDB  Type:PROTEIN  Length:672
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhh.eeeee.hhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhhh.........eeee.................eeeehhhhhhhhh........eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhh....hhhhhh............eee.hhhhhhhhhhheeeeeee.eeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5npp B  417 KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLG 1491
                                   426       436       446       456       466       476       486       496       506       516       526       536       580       590       600       610       620       630      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329      1339      1349      1359      1369      1379      1389      1399      1409      1419      1429      1439      1449      1459      1469      1479      1489  
                                                                                                                                                          545|                                                        639|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                                                                                           580                                                        1009                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  


Chain C from PDB  Type:DNA  Length:12
                                             
                5npp C    1 GTACCTACGGCT   12
                                    10  


Chain D from PDB  Type:PROTEIN  Length:671
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhh.eeeee.hhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh.eee........hhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhhh.........eeee.................eeeehhhhhhhhh........eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhh....hhhhhhhhh.........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
                5npp D  416 GKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYNERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQL 1490
                                   425       435       445       455       465       475       485       495       505       515       525       535       545|      589       599       609       619       629       639|     1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269      1279      1289      1299      1309      1319      1329      1339      1349      1359      1369      1379      1389      1399      1409      1419      1429      1439      1449      1459      1469      1479      1489 
                                                                                                                                                           545|                                                        639|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                                            580                                                        1010                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                


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


Chain F from PDB  Type:DNA  Length:8
                                         
                5npp F   -8 AGCCGTAG   -1
   Legend:   → Mismatch (orange background)
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  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 5NPP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5NPP)

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  5npp
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  GYRB_STAAN | P66937
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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 5iwm 5npk
        GYRB_STAAN | P66937: 2xco 2xcq 2xcr 2xcs 2xct 4bul 5cdm 5cdn 5cdo 5cdp 5cdq 5cdr 5iwi 5iwm 5npk

(-) Related Entries Specified in the PDB File

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