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 :  HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D SINGLE MUTANT M29F IN COMPLEX WITH DNA GCGA(UBR)CGC
 
Authors :  C. -Y. Chen, T. -P. Ko, T. -W. Lin, C. -C. Chou, C. -J. Chen, A. H. -J. Wang
Date :  29 Nov 04  (Deposition) - 22 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Complex Chromatin Protein/Dna, Minor-Groove Dna Binding, Archea, Kinked-Dna, Intercalation, Sac7D Mutant, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. -Y. Chen, T. -P. Ko, T. -W. Lin, C. -C. Chou, C. -J. Chen, A. H. -J. Wang
Probing The Dna Kink Structure Induced By The Hyperthermophilic Chromosomal Protein Sac7D
Nucleic Acids Res. V. 33 430 2005
PubMed-ID: 15653643  |  Reference-DOI: 10.1093/NAR/GKI191
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*GP*CP*GP*AP*(BRU)P*CP*GP*C)-3'
    Chains: C, D, E, F
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA-BINDING PROTEINS 7A/7B/7D
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: SULFOLOBUS ACIDOCALDARIUS
    Organism Taxid: 2285
    Synonym: 7 KD HYPERTHERMOPHILE DNA-BINDING PROTEIN, 7 KDA DNA-BINDING PROTEINS A/B/D, SAC7D

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1BRU4Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1WTP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WTP)

(-) 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:63
 aligned with DN7D_SULAC | P13123 from UniProtKB/Swiss-Prot  Length:66

    Alignment length:63
                                    11        21        31        41        51        61   
           DN7D_SULAC     2 VKVKFKYKGEEKEVDTSKIKKVWRVGKMVSFTYDDNGKTGRGAVSEKDAPKELLDMLARAERE  64
               SCOP domains d1wtpa_ A: automated matches                                    SCOP domains
               CATH domains 1wtpA00 A:2-64  [code=2.40.50.40, no name defined]              CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee...eeeeeee..eeeeeeee..eeeeeeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 1wtp A   2 VKVKFKYKGEEKEVDTSKIKKVWRVGKFVSFTYDDNGKTGRGAVSEKDAPKELLDMLARAERE  64
                                    11        21        31        41        51        61   


Chain B from PDB  Type:PROTEIN  Length:64
 aligned with DN7D_SULAC | P13123 from UniProtKB/Swiss-Prot  Length:66

    Alignment length:64
                                    11        21        31        41        51        61    
           DN7D_SULAC     2 VKVKFKYKGEEKEVDTSKIKKVWRVGKMVSFTYDDNGKTGRGAVSEKDAPKELLDMLARAEREK  65
               SCOP domains d1wtpb_ B: automated matches                                     SCOP domains
               CATH domains 1wtpB00 B:2-65  [code=2.40.50.40, no name defined]               CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee...eeeeeee..eeeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 1wtp B   2 VKVKFKYKGEEKEVDTSKIKKVWRVGKFVSFTYDDNGKTGRGAVSEKDAPKELLDMLARAEREK  65
                                    11        21        31        41        51        61    


Chain C from PDB  Type:DNA  Length:8
                                        
                 1wtp C 101 GCGAuCGC 108
                                |   
                              105-BRU


Chain D from PDB  Type:DNA  Length:8
                                        
                 1wtp D 109 GCGAuCGC 116
                                |   
                              113-BRU


Chain E from PDB  Type:DNA  Length:8
                                        
                 1wtp E 101 GCGAuCGC 108
                                |   
                              105-BRU


Chain F from PDB  Type:DNA  Length:8
                                        
                 1wtp F 109 GCGAuCGC 116
                                |   
                              113-BRU
   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 beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DN7D_SULAC | P13123)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
biological process
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.

 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
    BRU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1wtp)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wtp)
 

(-) 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
  1wtp
    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
  DN7D_SULAC | P13123
    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
  DN7D_SULAC | P13123
    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
        DN7D_SULAC | P13123: 1azp 1azq 1bf4 1ca5 1ca6 1sap 1wd0 1wd1 1wto 1wtq 1wtr 1wtv 1wtw 1wtx 1wvl 1xx8 1xyi 2xiw 4cj1 4cj2

(-) Related Entries Specified in the PDB File

1azp THE WILD-TYPE SAC7D COMPLEXED WITH DNA GCGATCGC
1wto SAC7D DOUBLE MUTANT V26F/M29F IN COMPLEX WITH DNA GCGATCGC
1wtq AC7D SINGLE MUTANT M29F IN COMPLEX WITH DNA GTAATTAC
1wtr SAC7D SINGLE MUTANT M29A IN COMPLEX WITH DNA GCGATCGC
1wtv SAC7D SINGLE MUTANT M29A IN COMPLEX WITH DNA GTAATTAC
1wtw SAC7D SINGLE MUTANT V26A IN COMPLEX WITH DNA GCGATCGC
1wtx SAC7D SINGLE MUTANT V26A IN COMPLEX WITH DNA GTAATTAC