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

(-) Description

Title :  THE PHAGE 434 OR2/R1-69 COMPLEX AT 2.5 ANGSTROMS RESOLUTION
 
Authors :  L. J. W. Shimon, S. C. Harrison
Date :  24 Mar 93  (Deposition) - 31 Jan 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,L,R
Keywords :  Protein-Dna Complex, Double Helix, Gene Regulation/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Shimon, S. C. Harrison
The Phage 434 Or2/R1-69 Complex At 2. 5 A Resolution.
J. Mol. Biol. V. 232 826 1993
PubMed-ID: 8355273  |  Reference-DOI: 10.1006/JMBI.1993.1434
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*TP*AP*TP*AP*CP*AP*AP*TP*GP*TP*AP*TP*CP*TP*TP*GP*T P*TP*TP*G)-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*AP*CP*AP*AP*AP*CP*AP*AP*GP*AP*TP*AP*CP*AP*TP*TP*G P*TP*AP*T)-3')
    Chains: A
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - PROTEIN (434 REPRESSOR)
    Chains: L, R
    Organism Scientific: PHAGE 434
    Organism Taxid: 10712

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABLR

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1RPE)

(-) Sites  (0, 0)

(no "Site" information available for 1RPE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CROC1PS50943 Cro/C1-type HTH domain profile.RPC1_BP4347-60
 		  2L:6-59
R:6-59

(-) Exons   (0, 0)

(no "Exon" information available for 1RPE)

(-) 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:20
                                                   
                  1rpe A 21 ACAAACAAGATACATTGTAT 40
                                    30        40


Chain B from PDB  Type:DNA  Length:20
                                                   
                  1rpe B  1 TATACAATGTATCTTGTTTG 20
                                    10        20


Chain L from PDB  Type:PROTEIN  Length:63
 aligned with RPC1_BP434 | P16117 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:63
                                    11        21        31        41        51        61   
            RPC1_BP434    2 SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRFLPELASALGVSVDWLLNGT 64
               SCOP domains d1rpel_ L: 434 C1 repressor, DNA-binding domain                 SCOP domains
               CATH domains 1rpeL00 L:1-63 lambda repressor-like DNA-binding domains        CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh....hhhhhhh....hhhhhhhhh........hhhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----HTH_CROC1  PDB: L:6-59 UniProt: 7-60                  ---- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  1rpe L  1 SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRFLPELASALGVSVDWLLNGT 63
                                    10        20        30        40        50        60   


Chain R from PDB  Type:PROTEIN  Length:63
 aligned with RPC1_BP434 | P16117 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:63
                                    11        21        31        41        51        61   
            RPC1_BP434    2 SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRFLPELASALGVSVDWLLNGT 64
               SCOP domains d1rper_ R: 434 C1 repressor, DNA-binding domain                 SCOP domains
               CATH domains 1rpeR00 R:1-63 lambda repressor-like DNA-binding domains        CATH domains
           Pfam domains (1) -----HTH_3-1rpeR01 R:6-59                                  ---- Pfam domains (1)
           Pfam domains (2) -----HTH_3-1rpeR02 R:6-59                                  ---- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhh....hhhhhhh....hhhhhhhhh........hhhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----HTH_CROC1  PDB: R:6-59 UniProt: 7-60                  ---- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  1rpe R  1 SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRFLPELASALGVSVDWLLNGT 63
                                    10        20        30        40        50        60
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain L,R   (RPC1_BP434 | P16117)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
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
(no "Ligands, Modified Residues, Ions" information available for 1rpe)
 
  Sites
(no "Sites" information available for 1rpe)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1rpe)
 

(-) 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)
Midas
  protein: ribbon, secondary structure; DNA: ribbon, plates
[ mono GIF format | stereo GIF format ]
Setor
  protein: ribbon; DNA: ribbon, sticks; chain-specific coloring
[ mono GIF format | stereo GIF format ]
  spacefill; chain-specific coloring
[ mono GIF format | stereo GIF format ]
  protein: ribbon, secondary structure; DNA: ribbon, sticks; chain-specific coloring
[ mono GIF format | stereo GIF format ]
  protein: ribbon, secondary structure, sticks; DNA: ribbon, sticks
[ mono GIF format | stereo GIF format ]
  protein: sticks; DNA: spacefill; detailed view
[ mono GIF format | stereo GIF format ]
  protein: spacefill; DNA: sticks; detailed view
[ mono GIF format | stereo GIF format ]
Distance Plot
  representative atoms: CA, O3'
[ mono GIF format | mono PDF format ]

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1rpe
    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
  RPC1_BP434 | P16117
    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
  RPC1_BP434 | P16117
    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
        RPC1_BP434 | P16117: 1per 1pra 1r63 1r69 1rpd 1sq8 2or1 2r63

(-) Related Entries Specified in the PDB File

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