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 :  STRUCTURAL INSIGHTS INTO THE UNIQUE SINGLE-STRANDED DNA BINDING MODE OF DNA PROCESSING PROTEIN A FROM HELICOBACTER PYLORI
 
Authors :  W. Wang
Date :  05 Jul 13  (Deposition) - 01 Jan 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dna Processing A Domain, Rossmann Fold, Ssdna Binding, Complex, Natural Recombination Mediating Protein, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Wang, J. Ding, Y. Zhang, Y. Hu, D. C. Wang
Structural Insights Into The Unique Single-Stranded Dna-Binding Mode Of Helicobacter Pylori Dpra.
Nucleic Acids Res. V. 42 3478 2014
PubMed-ID: 24369431  |  Reference-DOI: 10.1093/NAR/GKT1334

(-) Compounds

Molecule 1 - DNA PROCESSING CHAIN A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: HP0333, HP_0333
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695
 
Molecule 2 - SINGLE-STRANDED DNA
    Chains: C, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4LJR)

(-) Sites  (0, 0)

(no "Site" information available for 4LJR)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LJR)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:93 -Pro A:94
2Tyr A:108 -Pro A:109
3Leu B:93 -Pro B:94
4Tyr B:108 -Pro B:109

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LJR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LJR)

(-) Exons   (0, 0)

(no "Exon" information available for 4LJR)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee....hhhhhhh.......eeee.hhhhhh..eeee......hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhheeee........hhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhh...eee.......hhhhhhhhhh...ee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ljr A   5 MKSHFQYSTLENIPKAFDILKDPPKKLYCVGDTKLLDTPLKVAIIGTRRPTPYSKQHTITLARELAKNGAVIVSGGALGVDIIAQENALPKTIMLSPCSLDFIYPTNNHKVIQEIAQNGLILSEYEKDFMPIKGSFLARNRLVIALSDVVIIPQADLKSGSMSSARLAQKYQKPLFVLPQRLNESDGTNELLEKGQAQGIFNIQNFINTLLKD 217
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214   


Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee....hhhhhhh.......eeee.hhhhhh..eeee......hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh..eeeee........hhhhhhhhhhhhhhheeee........hhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhh...eee.......hhhhhhhhhh...ee..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ljr B   5 MKSHFQYSTLENIPKAFDILKDPPKKLYCVGDTKLLDTPLKVAIIGTRRPTPYSKQHTITLARELAKNGAVIVSGGALGVDIIAQENALPKTIMLSPCSLDFIYPTNNHKVIQEIAQNGLILSEYEKDFMPIKGSFLARNRLVIALSDVVIIPQADLKSGSMSSARLAQKYQKPLFVLPQRLNESDGTNELLEKGQAQGIFNIQNFINTLLKD 217
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214   


Chain C from PDB  Type:DNA  Length:6
                                      
                 4ljr C   1 TTTTTT   6


Chain D from PDB  Type:DNA  Length:1
                                 
                 4ljr D   1 T   5
   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 4LJR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LJR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LJR)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

 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 4ljr)
 
  Sites
(no "Sites" information available for 4ljr)
 
  Cis Peptide Bonds
    Leu A:93 - Pro A:94   [ RasMol ]  
    Leu B:93 - Pro B:94   [ RasMol ]  
    Tyr A:108 - Pro A:109   [ RasMol ]  
    Tyr B:108 - Pro B:109   [ RasMol ]  
 

(-) 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
  4ljr
    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
  O25100_HELPY | O25100
    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
  O25100_HELPY | O25100
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O25100_HELPY | O25100: 4ljk 4ljl

(-) Related Entries Specified in the PDB File

4ljk 4ljl