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(-) Description

Title :  TOPOISOMERASE IV ATP BINDING DOMAIN OF FRANCISELLA TULARENSIS IN COMPLEX WITH A SMALL MOLECULE INHIBITOR
 
Authors :  D. C Bensen, S. Akers-Rodriguez, T. Lam, L. W. Tari
Date :  15 May 13  (Deposition) - 15 Jan 14  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Atp-Binding, Nucleotide-Binding, Topoisomerase, Atp-Binding Domain, Dna Gyrase Negatively Supercoils Closed Circular Double-Stranded Dna, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. W. Tari, D. C. Bensen, J. Finn
A New Class Of Type Iia Topoisomerase Inhibitors With Broad-Spectrum Antibacterial Activity
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TOPOISOMERASE IV, SUBUNIT B
    Chains: A, B
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 18-224
    Gene: DNA TOPOISOMERASE IV SUBUNIT B PARE, FTL_1726, FTL_1726
    Organism Scientific: FRANCISELLA TULARENSIS SUBSP. HOLARCTICA
    Organism Taxid: 376619
    Strain: LVS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1DOO2Ligand/Ion6-FLUORO-4-[(3AR,6AR)-HEXAHYDROPYRROLO[3,4-B]PYRROL-5(1H)-YL]-N-METHYL-2-[(2-METHYLPYRIMIDIN-5-YL)OXY]-9H-PYRIMIDO[4,5-B]INDOL-8-AMINE
2IOD8Ligand/IonIODIDE ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1DOO1Ligand/Ion6-FLUORO-4-[(3AR,6AR)-HEXAHYDROPYRROLO[3,4-B]PYRROL-5(1H)-YL]-N-METHYL-2-[(2-METHYLPYRIMIDIN-5-YL)OXY]-9H-PYRIMIDO[4,5-B]INDOL-8-AMINE
2IOD6Ligand/IonIODIDE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1DOO1Ligand/Ion6-FLUORO-4-[(3AR,6AR)-HEXAHYDROPYRROLO[3,4-B]PYRROL-5(1H)-YL]-N-METHYL-2-[(2-METHYLPYRIMIDIN-5-YL)OXY]-9H-PYRIMIDO[4,5-B]INDOL-8-AMINE
2IOD2Ligand/IonIODIDE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:32 , GLN A:36 , HOH A:574BINDING SITE FOR RESIDUE IOD A 401
2AC2SOFTWAREASN A:41 , GLU A:45 , VAL A:66 , ASP A:68 , ARG A:71 , GLY A:72 , MET A:73 , ILE A:89 , VAL A:115 , THR A:162 , HOH A:501 , HOH A:533 , HOH A:582 , HOH A:602BINDING SITE FOR RESIDUE DOO A 403
3AC3SOFTWARELEU A:12BINDING SITE FOR RESIDUE IOD A 404
4AC4SOFTWARESER A:202 , ASN A:203BINDING SITE FOR RESIDUE IOD A 406
5AC5SOFTWAREASN B:32BINDING SITE FOR RESIDUE IOD B 401
6AC6SOFTWAREASN B:41 , SER B:42 , GLU B:45 , VAL B:66 , ASP B:68 , ARG B:71 , GLY B:72 , MET B:73 , PRO B:74 , VAL B:115 , THR B:162 , ILE B:164 , HOH B:511 , HOH B:516BINDING SITE FOR RESIDUE DOO B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:231 -Pro A:232

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KQV)

(-) 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:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4kqva1 A:7-215 automated matches                                                                                                                                                                      d4kqva2 A:216-380 automated matches                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....eeeeee.....eeeee...............hhhhhhhhheeeee.......hhhhhhheeeeeeeeee..eeeeeeee..eeeeeeeeeee......eeeeeeee.hhhh.....hhhhhhhhhhhhhhh....eeeeee....eeeee.......hhhhhh.....eeeeeee....eeeeeeee....eeeee..ee....hhhhhhhhhhhhhhhhhhhhh..........hhhhhhh.eeeeeeee.................hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kqv A   7 KSIEVLTGLDPVKKRPGMYTNIENPNHLIQEIIDNSVDEVLAGFASKINITLYEDNSIEVADDGRGMPVDIHPEHKMSGIELIMTKLHSGGKFSNGVGVSVVNALSTRLEAEIKRDGNVYHIVFEDGFKTKDLEIIDNVGKKNTGTKIRFWPNKKYFDDIKVNFKALKNLLEAKAILCKALTIKYSNEIKKEKLTWHFETGLKGYLDHKLPAEPFIIDNFSNGDSYLDAVFCWCESIKNSYVNLIPTPQDGTHVTGLKNGIYDAIKAYIEKNSLSVKNIKITANDSFAQLNYVISVKITNPQFAGQTKEKLSNKDVTNFVATAVKDLLTIWLNQNPDEARQIVENISKVAQKRIN 380
                                    16        26        36        46        56        66        76        86        96    || 116       126       136       146       156       166       176       186       196       206       216       231       241       251    || 265       275       285       295       305       315       325       335       345       355       365       375     
                                                                                                                        101|                                                                                                              225|                      256|                                                                                                                       
                                                                                                                         112                                                                                                               231                       261                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                    
               SCOP domains d4kqvb_ B: automated matches                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....eeeeee.....eeeee...............hhhhhhhhheee....hhhhhhhheeeeeeeeee..eeeeeeee..eeeeeeeeeee......eeeeeeee.hhhh.....hhhhhhhhhhhhhhhh...eeeeee....eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kqv B   8 SIEVLTGLDPVKKRPGMYTNIENPNHLIQEIIDNSVDEVLAGFASKINITLYEDNSIEVADDGRGMPVDIHPEHKMSGIELIMTKLHSGGKVGVSVVNALSTRLEAEIKRDGNVYHIVFEDGFKTKDLEIIDNVGKKNTGTKIRFWPNKKYFDDIKVNFKALKNLLEAKAILCKALTIKYSNEIKKEKLTWHFETG 217
                                    17        27        37        47        57        67        77        87        97||     121       131       141       151       161       171       181       191       201       211      
                                                                                                                     98|                                                                                                        
                                                                                                                     113
   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  (2, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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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
        PARE_FRATH | A0A0J9WZF0: 4hxz 4hy1 4hym

(-) Related Entries Specified in the PDB File

4hy1 4k4o 4kfg 4ksg 4ksh 4ktn