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(-)Theoretical Model
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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  P22 C2 REPRESSOR DIMER MODEL BOUND TO OPERATOR DNA
 
Authors :  R. Chattopadhyaya, K. Ghosh
Date :  22 Mar 99  (Deposition) - 23 Mar 99  (Release) - 23 Mar 99  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,C,D
Keywords :  Full P22 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 (5'- D(P*AP*TP*TP*TP*AP*AP*GP*AP*CP*TP*TP*CP*TP*TP*AP*AP*TP*T)- 3')
    Chains: A
    Engineered: YES
    Synonym: OPERATOR SITE OL1
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(P*AP*AP*TP*TP*AP*AP*GP*AP*AP*GP*TP*CP*TP*TP*AP*AP*AP*T)- 3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - PROTEIN (BACTERIOPHAGE P22 REPRESSOR)
    Chains: C, D
    Fragment: RESIDUES 1-216
    Organism Common: BACTERIOPHAGE P22

 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 1QAR)

(-) Sites  (0, 0)

(no "Site" information available for 1QAR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Theoretical Model
No.Residues
1Lys C:186 -Pro C:187
2Tyr C:192 -Pro C:193
3Lys D:186 -Pro D:187
4Tyr D:192 -Pro D:193

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Theoretical Model (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CROC1PS50943 Cro/C1-type HTH domain profile.RPC2_BPP2210-64
 		  2C:10-64
D:10-64

(-) Exons   (0, 0)

(no "Exon" information available for 1QAR)

(-) 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:18
                                                  
                 1qar A   1 ATTTAAGACTTCTTAATT  18
                                    10        


Chain B from PDB  Type:DNA  Length:18
                                                  
                 1qar B   1 AATTAAGAAGTCTTAAAT  18
                                    10        


Chain C from PDB  Type:PROTEIN  Length:216
 aligned with RPC2_BPP21 | P69203 from UniProtKB/Swiss-Prot  Length:5

    Alignment length:216
                                5                                                                                                                                                                                                                   
                                |    -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -      
           RPC2_BPP21     1 MNTQL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhh..............hhhhh..........hhhhhh.....hhhhhhhh.............................................ee............eee.....eee..........ee.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qar C   1 MNTQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGDLSQTNVAYHSRHEPRGSYPLISWVSAGQWMEAVEPYHKRAIENWHDTTVDCSEDSFWLDVQGDSMTAPAGLSIPEGMIILVDPEVEPRNGKLVVAKLEGENEATFKKLVMDAGRKFLKPLNPQYPMIEINGNCKIIGVVVDAKLANLP 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      


Chain C from PDB  Type:PROTEIN  Length:216
 aligned with RPC2_BPP22 | P69202 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
           RPC2_BPP22     1 MNTQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGDLSQTNVAYHSRHEPRGSYPLISWVSAGQWMEAVEPYHKRAIENWHDTTVDCSEDSFWLDVQGDSMTAPAGLSIPEGMIILVDPEVEPRNGKLVVAKLEGENEATFKKLVMDAGRKFLKPLNPQYPMIEINGNCKIIGVVVDAKLANLP 216
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhh..............hhhhh..........hhhhhh.....hhhhhhhh.............................................ee............eee.....eee..........ee.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------HTH_CROC1  PDB: C:10-64 UniProt: 10-64                 -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qar C   1 MNTQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGDLSQTNVAYHSRHEPRGSYPLISWVSAGQWMEAVEPYHKRAIENWHDTTVDCSEDSFWLDVQGDSMTAPAGLSIPEGMIILVDPEVEPRNGKLVVAKLEGENEATFKKLVMDAGRKFLKPLNPQYPMIEINGNCKIIGVVVDAKLANLP 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      


Chain D from PDB  Type:PROTEIN  Length:216
 aligned with RPC2_BPP21 | P69203 from UniProtKB/Swiss-Prot  Length:5

    Alignment length:216
                                5                                                                                                                                                                                                                   
                                |    -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -      
           RPC2_BPP21     1 MNTQL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhh.............................hhhhhh.....hhhhhhhh.............................................ee............eee.....eee..........ee.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qar D   1 MNTQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGDLSQTNVAYHSRHEPRGSYPLISWVSAGQWMEAVEPYHKRAIENWHDTTVDCSEDSFWLDVQGDSMTAPAGLSIPEGMIILVDPEVEPRNGKLVVAKLEGENEATFKKLVMDAGRKFLKPLNPQYPMIEINGNCKIIGVVVDAKLANLP 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      


Chain D from PDB  Type:PROTEIN  Length:216
 aligned with RPC2_BPP22 | P69202 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
           RPC2_BPP22     1 MNTQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGDLSQTNVAYHSRHEPRGSYPLISWVSAGQWMEAVEPYHKRAIENWHDTTVDCSEDSFWLDVQGDSMTAPAGLSIPEGMIILVDPEVEPRNGKLVVAKLEGENEATFKKLVMDAGRKFLKPLNPQYPMIEINGNCKIIGVVVDAKLANLP 216
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhh.............................hhhhhh.....hhhhhhhh.............................................ee............eee.....eee..........ee.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------HTH_CROC1  PDB: D:10-64 UniProt: 10-64                 -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qar D   1 MNTQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGDLSQTNVAYHSRHEPRGSYPLISWVSAGQWMEAVEPYHKRAIENWHDTTVDCSEDSFWLDVQGDSMTAPAGLSIPEGMIILVDPEVEPRNGKLVVAKLEGENEATFKKLVMDAGRKFLKPLNPQYPMIEINGNCKIIGVVVDAKLANLP 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 1QAR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 7)

Theoretical Model(hide GO term definitions)
Chain C,D   (RPC2_BPP22 | P69202)
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.

Chain C,D   (RPC2_BPP21 | P69203)
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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  Cis Peptide Bonds
    Lys C:186 - Pro C:187   [ RasMol ]  
    Lys D:186 - Pro D:187   [ RasMol ]  
    Tyr C:192 - Pro C:193   [ RasMol ]  
    Tyr D:192 - Pro D:193   [ RasMol ]  
 

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  RPC2_BPP22 | P69202
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 Related Entries

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

UniProtKB/Swiss-Prot
        RPC2_BPP22 | P69202: 1adr 2r1j 3jxb 3jxc 3jxd

(-) Related Entries Specified in the PDB File

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