Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE ATP BINDING DOMAIN OF S. AUREUS GYRB COMPLEXED WITH A FRAGMENT
 
Authors :  O. A. Andersen, J. Barker, A. T. Hadfield, R. K. Cheng, J. Kahmann, B. Fel M. Wood, C. Scheich, M. Mesleh, J. B. Cross, J. Zhang, Q. Yang, B. Lippa,
Date :  24 Jul 15  (Deposition) - 03 Feb 16  (Release) - 17 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dna Gyrase, Gyrb, Fragment-Based Screening, Structure-Based Design, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. F. Mesleh, J. B. Cross, J. Zhang, J. Kahmann, O. A. Andersen, J. Barker, R. K. Cheng, B. Felicetti, M. Wood, A. T. Hadfield, C. Scheich, T. I. Moy, Q. Yang, J. Shotwell, K. Nguyen, B. Lippa, R. Dolle, M. D. Ryan
Fragment-Based Discovery Of Dna Gyrase Inhibitors Targeting The Atpase Subunit Of Gyrb.
Bioorg. Med. Chem. Lett. V. 26 1314 2016
PubMed-ID: 26786695  |  Reference-DOI: 10.1016/J.BMCL.2016.01.009

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT B
    Chains: A, B
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24
    Expression System Strain: ROSETTA 2 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ATP BINDING DOMAIN, UNP RESIDUES 2-234 (DELTA105-127)
    Gene: GYRB
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 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  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
155D2Ligand/Ion2-(BUTANOYLAMINO)THIOPHENE-3-CARBOXAMIDE
2CL2Ligand/IonCHLORIDE ION
3MG2Ligand/IonMAGNESIUM ION
4MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
155D1Ligand/Ion2-(BUTANOYLAMINO)THIOPHENE-3-CARBOXAMIDE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
155D1Ligand/Ion2-(BUTANOYLAMINO)THIOPHENE-3-CARBOXAMIDE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:54 , GLU A:58 , ASP A:81 , ARG A:84 , ILE A:86 , HOH A:412 , HOH A:431 , HOH A:473binding site for residue 55D A 301
02AC2SOFTWAREGLU A:50 , HOH A:406 , HOH A:426 , HOH A:443 , HOH A:450 , HOH A:466binding site for residue MG A 302
03AC3SOFTWAREVAL A:88 , ARG A:144 , ASN A:145 , HOH A:499binding site for residue CL A 303
04AC4SOFTWARETHR A:80 , ASP A:81 , ASN A:82 , HIS A:143 , THR A:171 , HOH A:462binding site for residue MPD A 304
05AC5SOFTWAREGLY A:24 , VAL A:28 , TYR A:35 , SER A:128 , LEU A:205 , LYS A:207binding site for residue MPD A 305
06AC6SOFTWAREASN B:54 , GLU B:58 , ASP B:81 , ARG B:84 , GLY B:85 , ILE B:86 , PRO B:87 , HOH B:421 , HOH B:492binding site for residue 55D B 301
07AC7SOFTWAREGLU B:164 , GLU B:219 , HOH B:411 , HOH B:441binding site for residue MG B 302
08AC8SOFTWARELYS B:163 , TYR B:192 , GLU B:193 , ARG B:217 , HOH B:483binding site for residue CL B 303
09AC9SOFTWAREASP B:81 , LYS B:170 , MPD B:305 , MPD B:306 , HOH B:513binding site for residue MPD B 304
10AD1SOFTWAREHIS B:143 , GLU B:186 , THR B:187 , MPD B:304 , HOH B:439binding site for residue MPD B 305
11AD2SOFTWAREGLN B:66 , GLU B:68 , MPD B:304binding site for residue MPD B 306

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CTW)

(-) 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:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeeeehhheeeeee...............hhhhhhhhhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ctw A  16 AGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
                                    25        35        45        55        65        75        85        95       128       138       148       158       168       178       188       198       208       218       228  
                                                                                                                  104|                                                                                                      
                                                                                                                   128                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeeeehhheeeeee...............hhhhhhhhhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ctw B  17 GQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEG 231
                                    26        36        46        56        66        76        86        96       129       139       149       159       169       179       189       199       209       219       229  
                                                                                                                 104|                                                                                                       
                                                                                                                  128
   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  (0, 0)

(no "SCOP Domain" information available for 5CTW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    55D  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5ctw)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  5ctw
    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_STAAU | P0A0K8
    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_STAAU | P0A0K8
    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_STAAU | P0A0K8: 3g75 3g7b 3ttz 3u2d 3u2k 4plb 4urm 4uro 5bs3 5cph 5ctu 5ctx 5cty 5d6p 5d6q 5d7c 5d7d 5d7r 5iwi 5iwm

(-) Related Entries Specified in the PDB File

5cph 5ctu 5ctx 5cty