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(-) Description

Title :  THE DNA GYRASE B ATP BINDING DOMAIN OF ESCHERICHIA COLI IN COMPLEX WITH A SMALL MOLECULE INHIBITOR.
 
Authors :  D. C. Bensen, S. Akers-Rodriguez, T. Lam, L. W. Tari
Date :  26 Apr 13  (Deposition) - 15 Jan 14  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Atp-Binding, Nucleotide-Binding, Topoisomerase, Atp-Binding Domain, Isomerase-Isomerase Inhibitor Complex (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 - DNA GYRASE 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
    Gene: ACRB, HIMB, HISU, NALC, PARA, PCBA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
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
2SO43Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:79 , THR A:80 , GLY A:81 , ARG A:136 , GLU A:137 , HOH A:511 , HOH A:534BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREVAL A:111 , SER A:112 , GLY A:113 , HIS A:116 , HOH A:454 , HOH A:505 , HOH A:531 , HOH A:544 , HOH A:571 , GLY B:113 , ARG B:190BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREASN A:46 , GLU A:50 , VAL A:71 , ASP A:73 , ARG A:76 , GLY A:77 , ILE A:78 , PRO A:79 , MET A:91 , VAL A:120 , THR A:165 , HOH A:404 , HOH A:434 , HOH A:535 , HOH A:564BINDING SITE FOR RESIDUE DOO A 303
4AC4SOFTWAREPRO B:79 , THR B:80 , GLY B:81 , ARG B:136 , GLU B:137 , HOH B:483BINDING SITE FOR RESIDUE SO4 B 301
5AC5SOFTWAREASN B:46 , ASP B:49 , GLU B:50 , VAL B:71 , ASP B:73 , ARG B:76 , GLY B:77 , ILE B:78 , VAL B:120 , THR B:165 , HOH B:405 , HOH B:414 , HOH B:445 , HOH B:536 , HOH B:546BINDING SITE FOR RESIDUE DOO B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KFG)

(-) 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:189
                                                                                                                                                                                                                             
               SCOP domains d4kfga_ A: automated matches                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee..........hhhhhhhhh..........hhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kfg A  15 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIVSAAEVIMTVLKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYE 219
                                    24        34        44        54        64        74       |85       110       120       130       140       150       160       170       180       190       200       210         
                                                                                              82|        94|                                                                                                             
                                                                                               84        110                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains d4kfgb_ B: automated matches                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.....eeeee.....eeeee.........hhhhhhhhh..............hhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh....eeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kfg B  15 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGVSAAEVIMTVLDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHY 218
                                    24        34        44        54        64        74      ||86       107       117       127       137       147       157       167       177       187       197       207       217 
                                                                                             81|        94|                                                                                                                
                                                                                              84        106
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4kfg
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  GYRB_ECOLI | P0AES6
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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
        GYRB_ECOLI | P0AES6: 1aj6 1ei1 1kzn 3g7e 3nuh 4duh 4hyp 4prv 4prx 4pu9 4wub 4wuc 4wud 4xtj 4zvi 5l3j

(-) Related Entries Specified in the PDB File

4k4o