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(-) Description

Title :  1.9 A RESOLUTION REFINED STRUCTURE OF TBP RECOGNIZING THE MINOR GROOVE OF TATAAAAG
 
Authors :  J. L. Kim, S. K. Burley
Date :  06 Sep 96  (Deposition) - 06 Sep 96  (Release) - 06 Sep 96  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,_#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Protein-Dna Complex, Double Helix, Kinked (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Kim, S. K. Burley
1. 9 A Resolution Refined Structure Of Tbp Recognizing The Minor Groove Of Tataaaag
Nat. Struct. Biol. V. 1 638 1994
PubMed: search
(for further references see the PDB file header)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  1234567
Asymmetric/Biological Unit : ABCDEF_#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for PDT025)

(-) Sites  (0, 0)

(no "Site" information available for PDT025)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for PDT025)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:66 -Pro A:67
2Val A:157 -Pro A:158
3Glu B:1066 -Pro B:1067
4Val B:1157 -Pro B:1158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for PDT025)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for PDT025)

(-) Exons   (0, 0)

(no "Exon" information available for PDT025)

(-) 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:187
                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeee......hhhhhhh...eee..eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee......hhhhhhh..............eeeee....eeeee....eeeeeee..hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
              pdt025 A   12 VDLSKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKI  198
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       


Chain B from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                             
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeeee......hhhhhhh.............eeeee....eeeee....eeeeeee..hhhhhhhhhhhhhhhhh.......eeeeeeeeeeeee......hhhhhhh..............eeeee....eeeee....eeeeeee..hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
              pdt025 B 1011 PVDLSKHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAAFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMRDETYKAFENIYPVLSEFRKI 1198
                                  1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190        


Chain C from PDB  Type:DNA  Length:14
                                               
              pdt025 C  201 GCTATAAAAGGGCA  214
                                   210    


Chain D from PDB  Type:DNA  Length:14
                                               
              pdt025 D  215 TGCCCTTTTATAGC  228
                                   224    


Chain E from PDB  Type:DNA  Length:14
                                               
              pdt025 E  301 GCTATAAAAGGGCA  314
                                   310    


Chain F from PDB  Type:DNA  Length:14
                                               
              pdt025 F  315 TGCCCTTTTATAGC  328
                                   324
   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 PDT025)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for PDT025)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for PDT025)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:66 - Pro A:67   [ RasMol ]  
    Glu B:1066 - Pro B:1067   [ RasMol ]  
    Val A:157 - Pro A:158   [ RasMol ]  
    Val B:1157 - Pro B:1158   [ RasMol ]  
 

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 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 pdt009

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for PDT025)