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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPH PARE 24KDA IN COMPLEX WITH NOVOBIOCIN
 
Authors :  J. Lu, S. Patel, N. Sharma, S. Soisson, R. Kishii, M. Takei, Y. Fukuda, K. S. B. Singh
Date :  01 Jul 14  (Deposition) - 16 Jul 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Isomerase, Antibiotics, Gyrase, Natural Product (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Lu, S. Patel, N. Sharma, S. M. Soisson, R. Kishii, M. Takei, Y. Fukuda K. J. Lumb, S. B. Singh
Structures Of Kibdelomycin Bound To Staphylococcus Aureus Gyrb And Pare Showed A Novel U-Shaped Binding Mode.
Acs Chem. Biol. V. 9 2023 2014
PubMed-ID: 24992706  |  Reference-DOI: 10.1021/CB5001197

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE IV, B SUBUNIT
    Chains: A, B, C
    EC Number: 5.99.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PGEX-4T3
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN, RESIDUES 1-225
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: PARE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NOV3Ligand/IonNOVOBIOCIN
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NOV1Ligand/IonNOVOBIOCIN
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NOV1Ligand/IonNOVOBIOCIN
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1NOV1Ligand/IonNOVOBIOCIN

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:49 , ASP A:52 , GLU A:53 , ASP A:76 , ARG A:79 , GLY A:80 , MET A:81 , PRO A:82 , ILE A:96 , ARG A:138 , THR A:168 , HOH A:2001 , HOH A:2008 , ASP B:35 , LYS B:36 , ARG B:37 , NOV C:2000BINDING SITE FOR RESIDUE NOV A2000
2AC2SOFTWAREASN B:49 , ASP B:52 , GLU B:53 , ASP B:76 , ARG B:79 , GLY B:80 , MET B:81 , PRO B:82 , ILE B:96 , ARG B:138 , HOH B:2001 , HOH B:2009 , ASP C:35 , LYS C:36 , LYS C:180 , ASN C:186 , GLU C:192BINDING SITE FOR RESIDUE NOV B2000
3AC3SOFTWAREASP A:35 , LYS A:36 , VAL A:189 , NOV A:2000 , ASN C:49 , SER C:50 , GLU C:53 , ASP C:76 , ARG C:79 , GLY C:80 , MET C:81 , PRO C:82 , ILE C:96 , ARG C:138 , THR C:168 , HOH C:2003 , HOH C:2008BINDING SITE FOR RESIDUE NOV C2000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4URN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4URN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4URN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4URN)

(-) Exons   (0, 0)

(no "Exon" information available for 4URN)

(-) Sequences/Alignments

Asymmetric 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:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....eeeee..............hhhhhhhhh..hhhhhhhheeeeeeeeee..eeeeeeee...ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhhh..eeeeee......eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4urn A  17 LEGLEAVRKRPGMYIGSTDKRGLHHLVYEIVDNSVDEVLNGYGNEIDVTINKDGSISIEDNGRGMPTGIHKSGKPTVEVIFTVLVGASVVNALSEWLEVEIHRDGNIYHQSFKNGGSPSSGLVKKGKTKKTGTKVTFKPDDTIFKASTSFNFDVLSERLQESAFLLKNLKITLNDLRSGKERQEHYHY 223
                                    26        36        46        56        66        76        86        96   ||  125       135       145       155       165       175       185       195       205       215        
                                                                                                             100|                                                                                                       
                                                                                                              120                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee..............hhhhhhhhh..hhhhhhhhheeeeeeeeee..eeeeeeee...ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhhh..eeeeee......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4urn B  32 GSTDKRGLHHLVYEIVDNSVDEVLNGYGNEIDVTINKDGSISIEDNGRGMPTGIHKSGKPTVEVIFTVLGVGASVVNALSEWLEVEIHRDGNIYHQSFKNGGSPSSGLVKKGKTKKTGTKVTFKPDDTIFKASTSFNFDVLSERLQESAFLLKNLKITLNDLRSGKERQEHYHY 223
                                    41        51        61        71        81        91       119       129       139       149       159       169       179       189       199       209       219    
                                                                                              100|                                                                                                        
                                                                                               119                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee..............hhhhhhhhh.hhhhhhhheeeeeeeeee..eeeeeeee...ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhhh..eeeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4urn C  19 GLEAVRKRPGMYIGSTDKRGLHHLVYEIVDNSVDEVLNGYGNEIDVTINKDGSISIEDNGRGMPTGIHKSGKPTVEVIFTVLGASVVNALSEWLEVEIHRDGNIYHQSFKNGGSPSSGLVKKGKTKKTGTKVTFKPDDTIFKASTSFNFDVLSERLQESAFLLKNLKITLNDLRSGKERQEHYHYE 224
                                    28        38        48        58        68        78        88        98 ||    128       138       148       158       168       178       188       198       208       218      
                                                                                                           100|                                                                                                       
                                                                                                            121
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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 4URN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4URN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4URN)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4URN)

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 Related Entries

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(-) Related Entries Specified in the PDB File

4url CRYSTAL STRUCTURE OF STAPH PARE43KDA IN COMPLEX WITH KBD
4urm CRYSTAL STRUCTURE OF STAPH GYRASEB 24KDA IN COMPLEX WITH KIBDELOMYCIN
4uro CRYSTAL STRUCTURE OF STAPH GYRASEB 24KDA IN COMPLEX WITH NOVOBIOCIN