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

(-) Description

Title :  CRYSTAL STRUCTURE OF CHAETOMIUM THERMOPHILUM SKN7 WITH SSRE DNA
 
Authors :  T. Neudegger, J. Verghese, M. Hayer-Hartl, F. U. Hartl, A. Bracher
Date :  11 Aug 15  (Deposition) - 30 Dec 15  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,D,E
Keywords :  Protein-Dna Complex, Double Helix, Helix-Turn-Helix, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Neudegger, J. Verghese, M. Hayer-Hartl, F. U. Hartl, A. Bracher
Structure Of Human Heat-Shock Transcription Factor 1 In Complex With Dna.
Nat. Struct. Mol. Biol. V. 23 140 2016
PubMed-ID: 26727489  |  Reference-DOI: 10.1038/NSMB.3149

(-) Compounds

Molecule 1 - SSRE DNA STRAND 1
    Chains: A
    Engineered: YES
    Fragment: DNA BINDING DOMAIN
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synthetic: YES
 
Molecule 2 - SSRE DNA STRAND 2
    Chains: D
    Engineered: YES
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synthetic: YES
 
Molecule 3 - PUTATIVE TRANSCRIPTION FACTOR
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PHUE
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA 2
    Expression System Vector Type: PLASMID
    Gene: CTHT_0048700
    Organism Scientific: CHAETOMIUM THERMOPHILUM
    Organism Taxid: 209285
    Synonym: CTSKN7

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5D5X)

(-) Sites  (0, 0)

(no "Site" information available for 5D5X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D5X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D5X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D5X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D5X)

(-) Exons   (0, 0)

(no "Exon" information available for 5D5X)

(-) 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:DNA  Length:13
                                             
                 5d5x A   1 GGCCCAGCCAAAT  13
                                    10   


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..eee......eee.hhhhhhhhhhhhhhh..hhhhhhhhhhhh..ee............eeee.......hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 5d5x B  41 SDFVRKLYKMLEDPSYHSVVRWSDDGDSFVVLENEKFTKTILPKHFKHSNFASFVRQLNKYDFHKVRHNDEPYGRDAWEFKHPEFRADRKDNLDNIRRK 143
                                    50        60        70        80        90       100       110||     124       134         
                                                                                                111|                           
                                                                                                 116                           


Chain D from PDB  Type:DNA  Length:13
                                             
                 5d5x D   1 ATTTGGCTGGGCC  13
                                    10   


Chain E from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhh..eee......eee..hhhhhhhhhhhhh...hhhhhhhhhhhh..ee...........eeee..........hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 5d5x E  41 SDFVRKLYKMLEDPSYHSVVRWSDDGDSFVVLENEKFTKTILPKHFKHSNFASFVRQLNKYDFHKVRHNSPYGRDAWEFKHPEFRADRKDNLDNIRRK 143
                                    50        60        70        80        90       100       115       125       135        
                                                                                              109|                            
                                                                                               115
   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 5D5X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D5X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D5X)

(-) Gene Ontology  (6, 6)

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
(no "Ligands, Modified Residues, Ions" information available for 5d5x)
 
  Sites
(no "Sites" information available for 5d5x)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5d5x)
 

(-) 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 ](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
  5d5x
    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
  G0SB31_CHATD | G0SB31
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  G0SB31_CHATD | G0SB31
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        G0SB31_CHATD | G0SB31: 5d5w 5d5y 5d5z 5d60

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5D5X)