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 :  CRYSTAL STRUCTURE OF TETR-FAMILY TRANSCRIPTIONAL REGULATOR FROM STREPTOMYCES COELICOLOR
 
Authors :  R. Zhang, X. Xu, H. Zheng, A. Savchenko, A. Edwards, A. Joachimiak, Midw Center For Structural Genomics (Mcsg)
Date :  03 Jul 07  (Deposition) - 04 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tetr-Family Transcriptional Regulator, Hth Dna Binding, Structural Genomics, Mcsg, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Zhang, X. Xu, H. Zheng, A. Savchenko, A. Edwards, A. Joachimiak
The Crystal Structure Of Tetr-Family Transcriptional Regulator From Streptomyces Coelicolor.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TETR-FAMILY TRANSCRIPTIONAL REGULATOR
    AtccBAA-471
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPDM68
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    Organism ScientificSTREPTOMYCES COELICOLOR A3(2)
    Organism Taxid100226
    StrainA3(2), M145
    SynonymHTH DNA BINDING DOMAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2P6G4Ligand/IonHEXAETHYLENE GLYCOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:23 , PHE A:26 , TYR A:61 , ALA A:64 , LEU A:65 , PHE A:106 , VAL A:128 , GLU A:161BINDING SITE FOR RESIDUE P6G A 701
2AC2SOFTWARELEU B:72 , PHE B:76 , MSE B:92 , GLY B:105 , PHE B:106 , MSE B:110 , P6G B:704 , HOH B:771BINDING SITE FOR RESIDUE P6G B 702
3AC3SOFTWAREPHE A:76 , LEU A:88 , VAL A:91 , HIS A:139 , VAL A:183 , HIS A:184 , PHE A:186 , VAL A:207 , PHE A:217BINDING SITE FOR RESIDUE P6G A 703
4AC4SOFTWAREVAL B:91 , HIS B:139 , PHE B:186 , GLU B:211 , PRO B:216 , PHE B:217 , P6G B:702BINDING SITE FOR RESIDUE P6G B 704

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QIB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QIB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QIB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QIB)

(-) Exons   (0, 0)

(no "Exon" information available for 2QIB)

(-) 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:222
 aligned with Q9KZ14_STRCO | Q9KZ14 from UniProtKB/TrEMBL  Length:230

    Alignment length:222
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228  
         Q9KZ14_STRCO     9 MGVEERRQQLIGVALDLFSRRSPDEVSIDEIASAAGISRPLVYHYFPGKLSLYEAALQRASDDLADRFVEPRQGPLGARLLRVMGRYFDFVDEHGPGFSALMRGGPAVGSTTTNALVDSVRQAAYVQILSHLDVTEPPARLELVVRSWISLAESTALLWLDGRRIPRAELETQLVHDFAALMAVSAAYDEEMGALVRRVLADEPEDGPFGDLVDRLLALSAR 230
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains -2qibA00 A:10-230 Tetracycline Repressor, domain 2                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qib A   9 mGVEERRQQLIGVALDLFSRRSPDEVSIDEIASAAGISRPLVYHYFPGKLSLYEAALQRASDDLADRFVEPRQGPLGARLLRVmGRYFDFVDEHGPGFSALmRGGPAVGSTTTNALVDSVRQAAYVQILSHLDVTEPPARLELVVRSWISLAESTALLWLDGRRIPRAELETQLVHDFAALmAVSAAYDEEmGALVRRVLADEPEDGPFGDLVDRLLALSAR 230
                            |       18        28        38        48        58        68        78        88   |    98       108 |     118       128       138       148       158       168       178       188 |     198 |     208       218       228  
                            |                                                                                 92-MSE           110-MSE                                                                         190-MSE   200-MSE                          
                            9-MSE                                                                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:208
 aligned with Q9KZ14_STRCO | Q9KZ14 from UniProtKB/TrEMBL  Length:230

    Alignment length:215
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
         Q9KZ14_STRCO    14 RRQQLIGVALDLFSRRSPDEVSIDEIASAAGISRPLVYHYFPGKLSLYEAALQRASDDLADRFVEPRQGPLGARLLRVMGRYFDFVDEHGPGFSALMRGGPAVGSTTTNALVDSVRQAAYVQILSHLDVTEPPARLELVVRSWISLAESTALLWLDGRRIPRAELETQLVHDFAALMAVSAAYDEEMGALVRRVLADEPEDGPFGDLVDRLLALS 228
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qibB00 B:14-228 Tetracycline Repressor, domain 2                                                                                                                                                                       CATH domains
           Pfam domains (1) ----TetR_N-2qibB01 B:18-64                         -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----TetR_N-2qibB02 B:18-64                         -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh------hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....-hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qib B  14 RRQQLIGVALDLFSRRSPDEVSIDEIASAAGISRPLVYHYFPGKLSLYEAALQRASDDLADRFVEPRQGPLGARLLRVmGRYFDFVDEHGPGFSALmR------STTTNALVDSVRQAAYVQILSHLDVTEPPARLELVVRSWISLAESTALLWLDGRRIPRAELETQLVHDFAALmAVSAAYDEEmGALVRRVLADEPE-GPFGDLVDRLLALS 228
                                    23        33        43        53        63        73        83        93       103      || -    |  123       133       143       153       163       173       183      |193      |203       213 |     223     
                                                                                                         92-MSE           110-MSE 118                                                                     190-MSE   200-MSE      213 |             
                                                                                                                           111                                                                                                     215             

   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 2QIB)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9KZ14_STRCO | Q9KZ14)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    P6G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2qib)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2qib
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9KZ14_STRCO | Q9KZ14
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q9KZ14_STRCO | Q9KZ14
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2QIB)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2QIB)