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

(-) Description

Title :  PHAGE 434 REPRESSOR TETRAMER (TWO DIMERS) MODEL BOUND TO TWO ADJACENT OPERATOR DNA SITES
 
Authors :  R. Chattopadhyaya, K. Ghosh
Date :  19 Mar 99  (Deposition) - 22 Mar 99  (Release) - 26 Sep 01  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,C,D,E,F
Keywords :  Full 434 Repressor, Gene Regulation, Operator Sites (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Chattopadhyaya, K. Ghosh
The Common Three Dimensional Structure Of The Carboxy Terminal Domains Of Lambda, P22 And 434 Repressors
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (OPERATOR SITES OR1,OR2 AND INTERVENING BASE PAIRS)
    Chains: A
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (OPERATOR SITES OR1,OR2 AND INTERVENING BASE PAIRS)
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - PROTEIN (BACTERIOPHAGE 434 REPRESSOR RESIDUES 1- 209)
    Chains: C, D, E, F
    Organism Common: BACTERIOPHAGE 434

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1RPD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Theoretical Model
No.Residues
1Leu C:159 -Thr C:160
2Trp C:186 -Pro C:187
3Leu D:159 -Thr D:160
4Trp D:186 -Pro D:187
5Leu E:159 -Thr E:160
6Trp E:186 -Pro E:187
7Leu F:159 -Thr F:160
8Trp F:186 -Pro F:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Theoretical Model (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CROC1PS50943 Cro/C1-type HTH domain profile.RPC1_BP4347-60
 
 
 		  4C:6-59
D:6-59
E:6-59
F:6-59

(-) Exons   (0, 0)

(no "Exon" information available for 1RPD)

(-) Sequences/Alignments

Theoretical Model
   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:43
                                                                           
                 1rpd A   1 AAGTACAAACTTTCTTGTATTTTCATACAATGTATCTTGTTTG  43
                                    10        20        30        40   


Chain B from PDB  Type:DNA  Length:43
                                                                           
                 1rpd B   1 ACAAACAAGATACATTGTATGAAAATACAAGAAAGTTTGTACT  43
                                    10        20        30        40   


Chain C from PDB  Type:PROTEIN  Length:209
 aligned with RPC1_BP434 | P16117 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:209
                                                                                                                        95                                                                                                                   
                                    11        21        31        41        51        61        71        81        91   |     -         -         -         -         -         -         -         -         -         -         -         
           RPC1_BP434     2 SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRFLPELASALGVSVDWLLNGTSDSNVRFVGHVEPKGKYPLISMVRAGSWCEA-------------------------------------------------------------------------------------------------------------------   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhh.......hhhhhhhhhh.hhhhhhhh........eee..........eee...hhhhhh....hhhhhhhhh................................ee..............ee........eeee.....eee............................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----HTH_CROC1  PDB: C:6-59 UniProt: 7-60                  ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rpd C   1 SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRFLPELASALGVSVDWLLNGTSDSNVRFVGHVEPKGKYPLISMVRAGSWMEACEPYDIKDIAEWYDSDVNLLGNGFWLKVEGDSMTSPVGQSIPEGHMVLVDTGREPVNGSLVVAKLTDANEATFKKLVMDGGQKYLKGLNPSWPMTPINGNCKIIGVVVEARVKFV 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         


Chain D from PDB  Type:PROTEIN  Length:209
 aligned with RPC1_BP434 | P16117 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:209
                                                                                                                        95                                                                                                                   
                                    11        21        31        41        51        61        71        81        91   |     -         -         -         -         -         -         -         -         -         -         -         
           RPC1_BP434     2 SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRFLPELASALGVSVDWLLNGTSDSNVRFVGHVEPKGKYPLISMVRAGSWCEA-------------------------------------------------------------------------------------------------------------------   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhh.......hhhhhhh....hhhhhhhh........eee................hhhhhh....hhhhhhhhh................................ee..............ee.........eee.....eee............................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----HTH_CROC1  PDB: D:6-59 UniProt: 7-60                  ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rpd D   1 SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRFLPELASALGVSVDWLLNGTSDSNVRFVGHVEPKGKYPLISMVRAGSWMEACEPYDIKDIAEWYDSDVNLLGNGFWLKVEGDSMTSPVGQSIPEGHMVLVDTGREPVNGSLVVAKLTDANEATFKKLVMDGGQKYLKGLNPSWPMTPINGNCKIIGVVVEARVKFV 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         


Chain E from PDB  Type:PROTEIN  Length:209
 aligned with RPC1_BP434 | P16117 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:209
                                                                                                                        95                                                                                                                   
                                    11        21        31        41        51        61        71        81        91   |     -         -         -         -         -         -         -         -         -         -         -         
           RPC1_BP434     2 SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRFLPELASALGVSVDWLLNGTSDSNVRFVGHVEPKGKYPLISMVRAGSWCEA-------------------------------------------------------------------------------------------------------------------   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.......hhhhhhhhh..hhhhhhhh........eee..........eee...hhhhhh....hhhhhhhhh................................ee..............ee........eeee.....eee............................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----HTH_CROC1  PDB: E:6-59 UniProt: 7-60                  ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rpd E   1 SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRFLPELASALGVSVDWLLNGTSDSNVRFVGHVEPKGKYPLISMVRAGSWMEACEPYDIKDIAEWYDSDVNLLGNGFWLKVEGDSMTSPVGQSIPEGHMVLVDTGREPVNGSLVVAKLTDANEATFKKLVMDGGQKYLKGLNPSWPMTPINGNCKIIGVVVEARVKFV 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         


Chain F from PDB  Type:PROTEIN  Length:209
 aligned with RPC1_BP434 | P16117 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:209
                                                                                                                        95                                                                                                                   
                                    11        21        31        41        51        61        71        81        91   |     -         -         -         -         -         -         -         -         -         -         -         
           RPC1_BP434     2 SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRFLPELASALGVSVDWLLNGTSDSNVRFVGHVEPKGKYPLISMVRAGSWCEA-------------------------------------------------------------------------------------------------------------------   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh.......hhhhhhhhhh.hhhhhhhh........eee................hhhhhh....hhhhhhhhh................................ee..............ee.........eee.....eee............................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----HTH_CROC1  PDB: F:6-59 UniProt: 7-60                  ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rpd F   1 SISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRFLPELASALGVSVDWLLNGTSDSNVRFVGHVEPKGKYPLISMVRAGSWMEACEPYDIKDIAEWYDSDVNLLGNGFWLKVEGDSMTSPVGQSIPEGHMVLVDTGREPVNGSLVVAKLTDANEATFKKLVMDGGQKYLKGLNPSWPMTPINGNCKIIGVVVEARVKFV 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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 1RPD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1RPD)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Theoretical Model(hide GO term definitions)
Chain C,D,E,F   (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

Theoretical Model
  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 1rpd)
 
  Sites
(no "Sites" information available for 1rpd)
 
  Cis Peptide Bonds
    Leu C:159 - Thr C:160   [ RasMol ]  
    Leu D:159 - Thr D:160   [ RasMol ]  
    Leu E:159 - Thr E:160   [ RasMol ]  
    Leu F:159 - Thr F:160   [ RasMol ]  
    Trp C:186 - Pro C:187   [ RasMol ]  
    Trp D:186 - Pro D:187   [ RasMol ]  
    Trp E:186 - Pro E:187   [ RasMol ]  
    Trp F:186 - Pro F:187   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Theoretical Model 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
  1rpd
    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 1rpe 1sq8 2or1 2r63

(-) Related Entries Specified in the PDB File

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