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(-) Description

Title :  CRYSTAL STRUCTURE OF S.A. GYRASE IN COMPLEX WITH COMPOUND 7
 
Authors :  J. Lu, S. Patel, S. Soisson
Date :  01 Jun 15  (Deposition) - 17 Jun 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  B,D,E,F
Keywords :  Gyrase, Antibacterial, Sar, Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. B. Singh, D. E. Kaelin, J. Wu, L. Miesel, C. M. Tan, T. Black, R. Nargund, P. T. Meinke, D. B. Olsen, A. Lagrutta, J. Lu, S. Patel, K. W. Rickert, R. F. Smith, S. Soisson, E. Sherer, L. A. Joyce, C. Wei, X. Peng, X. Wang, H. Fukuda, R. Kishii, M. Takei, H. Takano, M. Shibasaki, M. Yajima, A. Nishimura, T. Shibata, Y. Fukuda
Tricyclic 1, 5-Naphthyridinone Oxabicyclooctane-Linked Novel Bacterial Topoisomerase Inhibitors As Broad-Spectrum Antibacterial Agents-Sar Of Left-Hand-Side Moiety (Part-2).
Bioorg. Med. Chem. Lett. V. 25 1831 2015
PubMed-ID: 25851938  |  Reference-DOI: 10.1016/J.BMCL.2015.03.044

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT A AND B
    Chains: B, D
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GYRB, GYRA
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
 
Molecule 2 - DNA/RNA (5'-R(P*AP*GP*CP*CP*G)-D(P*T)- R(P*AP*GP*GP*GP*CP*CP*C)-D(P*T)-R(P*AP*CP*GP*GP*C)-D(P*T)-3')
    Chains: E, F
    Engineered: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS ED98
    Organism Taxid: 681288
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : BDEF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2SO43Ligand/IonSULFATE ION
3WCP1Ligand/Ion(4R)-3-FLUORO-4-HYDROXY-4-{[(1R,4R)-4-{[(3-OXO-3,4-DIHYDRO-2H-PYRIDO[3,2-B][1,4]OXAZIN-6-YL)METHYL]AMINO}-2-OXABICYCLO[2.2.2]OCT-1-YL]METHYL}-4,5-DIHYDRO-7H-PYRROLO[3,2,1-DE][1,5]NAPHTHYRIDIN-7-ONE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:435 , ASP B:508 , HOH B:1602 , HOH B:1606 , G E:8 , G E:9binding site for residue MN B 1501
2AC2SOFTWAREGLU D:435 , ASP D:508 , HOH D:1605 , HOH D:1618 , G F:8 , G F:9binding site for residue MN D 1501
3AC3SOFTWAREARG B:1429 , ARG D:1429 , ARG D:1432 , HOH D:1612binding site for residue SO4 D 1502
4AC4SOFTWAREG E:5 , DT E:6 , A F:15binding site for residue SO4 E 101
5AC5SOFTWAREALA B:1068 , GLY B:1072 , MET B:1075 , ASP B:1083 , MET B:1121 , ALA D:1068 , GLY D:1072 , MET D:1075 , ASP D:1083 , G E:10 , C E:11 , G F:10 , C F:11binding site for residue WCP F 101
6AC6SOFTWAREDT E:14 , A E:15 , G F:5 , DT F:6 , A F:7binding site for residue SO4 F 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BS3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5BS3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BS3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BS3)

(-) Exons   (0, 0)

(no "Exon" information available for 5BS3)

(-) 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 B from PDB  Type:PROTEIN  Length:670
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.hhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....eee....hhhhhhhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhhhh........eeee.................eeeehhhhhhhh.........eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhh............eee.hhhhhhhhhhheeeeeee.eeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh.....eeeeee.........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5bs3 B  417 KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYNERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQL 1490
                                   426       436       446       456       466       476       486       496       506       516       526       536       580       590       600       610       620       630      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350      1360      1370      1380      1390      1400      1410      1420      1430      1440      1450      1460      1470      1480      1490
                                                                                                                                                          545|                                                        639|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                                           580                                                        1010                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:670
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhh.eeeee.hhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhh.......hhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.........eehhhhhhhhhhhh...hhhhhhhhhhhhhh........eeee.................eeeehhhhhhhhh........eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...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
                5bs3 D  417 KLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPTGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYNERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDRRTEIQL 1490
                                   426       436       446       456       466       476       486       496       506       516       526       536       580       590       600       610       620       630      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350      1360      1370      1380      1390      1400      1410      1420      1430      1440      1450      1460      1470      1480      1490
                                                                                                                                                          545|                                                        639|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                                           580                                                        1010                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                


Chain E from PDB  Type:DNA  Length:20
                                                     
                5bs3 E    1 AGCCGTAGGGCCCTACGGCT   20
                                    10        20


Chain F from PDB  Type:DNA  Length:19
                                                    
                5bs3 F    1 AGCCGTAGGGCCCTACGGC   19
                                    10
   Legend:   → Mismatch (orange background)
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    → 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 5BS3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5BS3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BS3)

(-) Gene Ontology  (14, 25)

Asymmetric/Biological Unit(hide GO term definitions)

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  GYRB_STAAU | P0A0K8
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 Related Entries

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

UniProtKB/Swiss-Prot
        GYRA_STAAU | P20831: 4plb
        GYRB_STAAU | P0A0K8: 3g75 3g7b 3ttz 3u2d 3u2k 4plb 4urm 4uro 5cph 5ctu 5ctw 5ctx 5cty 5d6p 5d6q 5d7c 5d7d 5d7r 5iwi 5iwm

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