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

(-) Description

Title :  STRUCTURE OF N15 CRO COMPLEXED WITH CONSENSUS OPERATOR DNA
 
Authors :  B. M. Hall, S. A. Roberts, M. H. J. Cordes
Date :  28 Feb 11  (Deposition) - 29 Feb 12  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,N
Keywords :  Structural Evolution, Helix-Turn-Helix, Lambda Repressor-Like Dna- Binding Domain, Phage Repressor, Transcription Factor, Repressor, Dna Binding, Transcription Repressor-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. M. Hall, S. A. Roberts, D. J. O'Brien, M. S. Dubrava, M. H. J. Cordes
Mysteries Of An Evolutionary Code: The Structure Of N15 Cro Complexed With Operator Dna
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GP39
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMD104 (PET21B-DERIVED)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CRO, GENE 39
    Organism Scientific: ENTEROBACTERIA PHAGE N15
    Organism Taxid: 40631
    Synonym: REPRESSOR PROTEIN
 
Molecule 2 - 5'-D(*TP*TP*TP*AP*TP*AP*GP*CP*TP*AP*GP*CP*TP*AP*TP*AP*A)- 3'
    Chains: C, N
    Engineered: YES
    Organism Scientific: ENTEROBACTERIA PHAGE N15
    Organism Taxid: 40631
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCN

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3QWS)

(-) Sites  (0, 0)

(no "Site" information available for 3QWS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QWS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QWS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QWS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QWS)

(-) Exons   (0, 0)

(no "Exon" information available for 3QWS)

(-) 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:62
 aligned with Q37964_BPN15 | Q37964 from UniProtKB/TrEMBL  Length:71

    Alignment length:62
                                    10        20        30        40        50        60  
          Q37964_BPN15    1 MKPEELVRHFGDVEKAAVGVGVTPGAVYQWLQAGEIPPLRQSDIEVRTAYKLKSDFTSQRMG 62
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  3qws A  1 MKPEELVRHFGDVEKAAVGVGVTPGAVYQWLQAGEIPPLRQSDIEVRTAYKLKSDFTSQRMG 62
                                    10        20        30        40        50        60  


Chain B from PDB  Type:PROTEIN  Length:63
 aligned with Q37964_BPN15 | Q37964 from UniProtKB/TrEMBL  Length:71

    Alignment length:63
                                    10        20        30        40        50        60   
          Q37964_BPN15    1 MKPEELVRHFGDVEKAAVGVGVTPGAVYQWLQAGEIPPLRQSDIEVRTAYKLKSDFTSQRMGK 63
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  3qws B  1 MKPEELVRHFGDVEKAAVGVGVTPGAVYQWLQAGEIPPLRQSDIEVRTAYKLKSDFTSQRMGK 63
                                    10        20        30        40        50        60   


Chain C from PDB  Type:DNA  Length:17
                                                
                  3qws C  1 TTTATAGCTAGCTATAA 17
                                    10       


Chain N from PDB  Type:DNA  Length:17
                                                
                  3qws N  1 TTTATAGCTAGCTATAA 17
                                    10
   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 3QWS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QWS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QWS)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q37964_BPN15 | Q37964)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

 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 3qws)
 
  Sites
(no "Sites" information available for 3qws)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3qws)
 

(-) 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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3qws
    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
  Q37964_BPN15 | Q37964
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q37964_BPN15 | Q37964
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q37964_BPN15 | Q37964: 2hin

(-) Related Entries Specified in the PDB File

2hin STRUCTURE OF N15 CRO AT 1.05 A