Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  PYRROLOPYRIMIDINE INHIBITORS OF DNA GYRASE B AND TOPOISOMERASE IV, PART I: STRUCTURE GUIDED DISCOVERY AND OPTIMIZATION OF DUAL TARGETING AGENTS WITH POTENT, BROAD-SPECTRUM ENZYMATIC ACTIVITY.
 
Authors :  D. C. Bensen, Z. Chen, L. W. Tari
Date :  01 Aug 12  (Deposition) - 13 Feb 13  (Release) - 27 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Atp-Binding, Nucleotide-Binding, Topoisomerase, Atp-Binding Domain, Dna Gyrase Negatively Supercoils Closed Circular Double-Stranded Dna In An Atp-Dependent Manner And Also Catalyzes The Interconversion Of Other Topological Isomers Of Double-Stranded Dna Rings, Isomerase- Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. W. Tari, M. Trzoss, D. C. Bensen, X. Li, Z. Chen, T. Lam, J. Zhang, C. J. Creighton, M. L. Cunningham, B. Kwan, M. Stidham, K. J. Shaw, F. C. Lightstone, S. E. Wong, T. B. Nguyen, J. Nix, J. Finn
Pyrrolopyrimidine Inhibitors Of Dna Gyrase B (Gyrb) And Topoisomerase Iv (Pare). Part I: Structure Guided Discovery And Optimization Of Dual Targeting Agents With Potent, Broad-Spectrum Enzymatic Activity.
Bioorg. Med. Chem. Lett. V. 23 1529 2013
PubMed-ID: 23352267  |  Reference-DOI: 10.1016/J.BMCL.2012.11.032

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT B
    Chains: A
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: GYRB, EF_0005
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 226185
    Strain: ATCC 700802 / V583

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
10WT1Ligand/Ion(1R,5S,6S)-3-[5-CHLORO-6-ETHYL-2-(PYRIMIDIN-5-YLOXY)-7H-PYRROLO[2,3-D]PYRIMIDIN-4-YL]-3-AZABICYCLO[3.1.0]HEXAN-6-AMINE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:48 , SER A:49 , GLU A:52 , ASP A:75 , ARG A:78 , GLY A:79 , ILE A:80 , PRO A:81 , GLY A:119 , SER A:122 , THR A:167 , HOH A:407 , HOH A:483BINDING SITE FOR RESIDUE 0WT A 301
2AC2SOFTWAREALA A:53 , THR A:130 , ARG A:148 , ARG A:149 , ASN A:200 , ARG A:201 , LEU A:203 , HOH A:476BINDING SITE FOR RESIDUE GOL A 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GEE)

(-) 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:193
                                                                                                                                                                                                                                 
               SCOP domains d4geea_ A: automated matches                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee...............hhhhhhhhh....hhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee......eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gee A  18 GLEAVRKRPGMYIGSTSGEGLHHLVWEIVDNSIDEALAGFAKSIQVIIEPDDSITVIDDGRGIPVGIQAKTGRPAVETVFTVLHGVGSSVVNALSTSLDVRVYKDGKVYYQEYRRGAVVDDLKVIEETDRHGTTVHFIPDPEIFTETTVYDFDKLATRVRELAFLNRGLHISIEDRREGQEDKKEYHYEGLEH 227
                                    27        37        47        57        67        77        87        97   ||  124       134       144       154       164       174       184       194       204       214       224   
                                                                                                             101|                                                                                                            
                                                                                                              119
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    0WT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4gee)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4gee
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GYRB_ENTFA | Q839Z1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  5.99.1.3
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  GYRB_ENTFA | Q839Z1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GYRB_ENTFA | Q839Z1: 4gfn 4ggl 4hxw 4k4o 4ksg 4ksh 4ktn

(-) Related Entries Specified in the PDB File

4gfn 4ggl 4hxw 4hxz 4hy1 4hym 4hyp 4hz0 4hz5