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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  WILD TYPE GENE-REGULATING PROTEIN ARC/DNA COMPLEX
 
Authors :  J. F. Schilbach, A. W. Karzai, B. E. Raumann, R. T. Sauer
Date :  11 May 98  (Deposition) - 16 Feb 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Gene-Regulating Protein, Gene Regulation/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. F. Schildbach, A. W. Karzai, B. E. Raumann, R. T. Sauer
Origins Of Dna-Binding Specificity: Role Of Protein Contacts With The Dna Backbone.
Proc. Natl. Acad. Sci. Usa V. 96 811 1999
PubMed-ID: 9927650  |  Reference-DOI: 10.1073/PNAS.96.3.811
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*TP*AP*TP*AP*GP*TP*AP*GP*AP*GP*TP*GP*CP*TP*TP*CP*TP*AP*TP *CP*AP*T)-3')
    Chains: E
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*AP*AP*TP*GP*AP*TP*AP*GP*AP*AP*GP*CP*AP*CP*TP*CP*TP*AP*CP *TP*AP*T)-3')
    Chains: F
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - PROTEIN (GENE-REGULATING PROTEIN ARC)
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ENTEROBACTERIA PHAGE P22
    Organism Taxid: 10754
    Other Details: SYNTHETIC GENE

 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 1BDT)

(-) Sites  (0, 0)

(no "Site" information available for 1BDT)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BDT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BDT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BDT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1BDT)

(-) Exons   (0, 0)

(no "Exon" information available for 1BDT)

(-) 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:52
 aligned with RARC_BPP22 | P03050 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:52
                                    10        20        30        40        50  
            RARC_BPP22    1 MKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIG 52
               SCOP domains d1bdta_ A: Arc repressor                             SCOP domains
               CATH domains 1bdtA00 A:1-52 Met repressor-like                    CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeehhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                  1bdt A  1 MKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIG 52
                                    10        20        30        40        50  


Chain B from PDB  Type:PROTEIN  Length:53
 aligned with RARC_BPP22 | P03050 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:53
                                    10        20        30        40        50   
            RARC_BPP22    1 MKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIGA 53
               SCOP domains d1bdtb_ B: Arc repressor                              SCOP domains
               CATH domains 1bdtB00 B:1-53 Met repressor-like                     CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeehhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  1bdt B  1 MKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIGA 53
                                    10        20        30        40        50   


Chain C from PDB  Type:PROTEIN  Length:50
 aligned with RARC_BPP22 | P03050 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:50
                                    10        20        30        40        50
            RARC_BPP22    1 MKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGR 50
               SCOP domains d1bdtc_ C: Arc repressor                           SCOP domains
               CATH domains 1bdtC00 C:1-50 Met repressor-like                  CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeehhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1bdt C  1 MKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGR 50
                                    10        20        30        40        50


Chain D from PDB  Type:PROTEIN  Length:50
 aligned with RARC_BPP22 | P03050 from UniProtKB/Swiss-Prot  Length:53

    Alignment length:50
                                    10        20        30        40        50
            RARC_BPP22    1 MKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGR 50
               SCOP domains d1bdtd_ D: Arc repressor                           SCOP domains
               CATH domains 1bdtD00 D:1-50 Met repressor-like                  CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeehhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  1bdt D  1 MKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGR 50
                                    10        20        30        40        50


Chain E from PDB  Type:DNA  Length:22
                                                     
                  1bdt E  1 TATAGTAGAGTGCTTCTATCAT 22
                                    10        20  


Chain F from PDB  Type:DNA  Length:22
                                                     
                  1bdt F  1 AATGATAGAAGCACTCTACTAT 22
                                    10        20
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BDT)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (RARC_BPP22 | P03050)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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.

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  1bdt
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  RARC_BPP22 | P03050
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 Related Entries

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

UniProtKB/Swiss-Prot
        RARC_BPP22 | P03050: 1arq 1arr 1b28 1baz 1bdv 1myk 1myl 1nla 1par 1qtg 1u9p

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BDT)