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 :  CO-CRYSTAL STRUCTURE OF TBP RECOGNIZING THE MINOR GROOVE OF A TATA ELEMENT
 
Authors :  J. L. Kim, D. B. Nikolov, S. K. Burley
Date :  17 Dec 93  (Deposition) - 17 Dec 93  (Release) - 21 Sep 01  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Protein-Dna Complex, Double Helix (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Kim, D. B. Nikolov, S. K. Burley
Co-Crystal Structure Of Tbp Recognizing The Minor Groove Of A Tata Element
Nature V. 365 520 1993
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*A)-3')
    Chains: A, C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*TP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*C)-3')
    Chains: B, D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - TATA BINDING PROTEIN (TBP)
    Chains: E, F
    Genus: ARABIDOPSIS
    Organism Common: FLOWER
    Organism Scientific: ARABIDOPSIS THALIANA
    Species: THALIANA

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for PDT009)

(-) Sites  (0, 0)

(no "Site" information available for PDT009)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for PDT009)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu E:66 -Pro E:67
2Val E:157 -Pro E:158
3Glu F:66 -Pro F:67
4Val F:157 -Pro F:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for PDT009)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for PDT009)

(-) Exons   (0, 0)

(no "Exon" information available for PDT009)

(-) 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:14
                                              
               pdt009 A 201 GCTATAAAAGGGCA 214
                                   210    


Chain B from PDB  Type:DNA  Length:14
                                              
               pdt009 B 301 TGCCCTTTTATAGC 314
                                   310    


Chain C from PDB  Type:DNA  Length:14
                                              
               pdt009 C 401 GCTATAAAAGGGCA 414
                                   410    


Chain D from PDB  Type:DNA  Length:14
                                              
               pdt009 D 501 TGCCCTTTTATAGC 514
                                   510    


Chain E from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeeeeeee.....hhhhhhhhh..ee........eeeee....eeeee....eeeeeee.hhhhhhhhhhhhhhhhhh.......eeeeeeeeeeeee.....hhhhhhhhh...ee........eeeee....eeeee....eeeeeee.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
               pdt009 E  13 DLSKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKI 198
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192      


Chain F from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeeeeeee.....hhhhhhhhh...ee.......eeeee....eeeee....eeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeeeeeeeee.....hhhhhhhhh...ee........eeee......eeee....eeeeeee.hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
               pdt009 F  13 DLSKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKI 198
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192
   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 PDT009)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for PDT009)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for PDT009)

(-) 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 pdt009)
 
  Sites
(no "Sites" information available for pdt009)
 
  Cis Peptide Bonds
    Glu E:66 - Pro E:67   [ RasMol ]  
    Glu F:66 - Pro F:67   [ RasMol ]  
    Val E:157 - Pro E:158   [ RasMol ]  
    Val F:157 - Pro F:158   [ RasMol ]  
 

(-) 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
  pdt009
    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
  TBP1_ARATH | P28147
    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)
  (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
  TBP1_ARATH | P28147
    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
        TBP1_ARATH | P28147: 1qn3 1qn4 1qn5 1qn6 1qn7 1qn8 1qn9 1qna 1qnb 1qnc 1qne 1vok 1vol 1vtl 1vto pdt025

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for PDT009)