Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF DDRB FROM DEINOCOCCUS RADIODURANS BOUND TO SSDNA
 
Authors :  S. N. Sugiman-Marangos, M. S. Junop
Date :  25 Oct 12  (Deposition) - 04 Sep 13  (Release) - 04 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,M,N
Biol. Unit 1:  A,B,C,D,E,M,N  (1x)
Biol. Unit 2:  A,B,C,D,E,M,N  (2x)
Keywords :  Dna Annealing, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. N. Sugiman-Marangos, J. K. Peel, Y. M. Weiss, R. Ghirlando, M. S. Junop
Crystal Structure Of The Ddrb/Ssdna Complex From Deinococcu Radiodurans Reveals A Dna Binding Surface Involving Higher-Order Oligomeric States.
Nucleic Acids Res. V. 41 9934 2013
PubMed-ID: 23975200  |  Reference-DOI: 10.1093/NAR/GKT759

(-) Compounds

Molecule 1 - SINGLE-STRANDED DNA-BINDING PROTEIN DDRB
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET151/D-TOPO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DDRB, DDRB (DR0070), DR_0070
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Synonym: DNA DAMAGE RESPONSE PROTEIN B
 
Molecule 2 - 5'-D(*TP*TP*TP*T)-3'
    Chains: M
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(P*TP*TP*TP*TP*T)-3'
    Chains: N
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEMN
Biological Unit 1 (1x): ABCDEMN
Biological Unit 2 (2x): ABCDEMN

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4HQB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:93 -Lys A:94

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HQB)

(-) Sequences/Alignments

Asymmetric 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:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee.hhhhhhhhhhhhhh............eeehhhhh...hhhhhh.eeeee...eeeeee..eeeeeeee..eee..eee..eeeeeee.....hhhhh........eeeeeee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hqb A   1 MLQIEFITDLGARVTVNVEHESRLLDVQRHYGRLGWTSGEIPSGGYQFPIENEADFDWSLIGARKWKSPEGEELVIHRGHAYRRRELEAVDSRKLKLPAAIKYSRGAKVSDPQHVREKADGDIEYVSLAIFRGGKRQERYAVP 143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   


Chain B from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee.hhhhhhhhhhhhhh............eeehhhhh...hhhhh.eeeee.....eeeee..eeeeeeee....eeeeeee.....hhhhh....eeeeeee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hqb B   1 MLQIEFITDLGARVTVNVEHESRLLDVQRHYGRLGWTSGEIPSGGYQFPIENEADFDWSLIGARKWKSPEGEELVIHRGHAYRRRELEAPAAIKYSRGAKVSDPQHVREKIEYVSLAIFRGGKRQERYAVP 143
                                    10        20        30        40        50        60        70        80        98       108       118|      132       142 
                                                                                                                   89|                 118|                    
                                                                                                                    98                  123                    


Chain C from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee.hhhhhhhhhhhhhh............eeehhhhh...hhhhh.ee...eee..eeeeee....eeeee............eeeeeee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 4hqb C   1 MLQIEFITDLGARVTVNVEHESRLLDVQRHYGRLGWTSGEIPSGGYQFPIENEADFDWSLIGARKWLVIHRGHAYRRRELEIKYSRGAKVSDPQHVREEYVSLAIFRGGKRQERYAVP 143
                                    10        20        30        40        50        60     || 77        87||     109       125       135        
                                                                                            66|            88|             117|                   
                                                                                             74            101              124                   


Chain D from PDB  Type:PROTEIN  Length:109
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee.hhhhhhhhhhhhhh............eeehhhhh...hhhhhh.eeee.....eeeee..eeee..eee....eeeee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 4hqb D   1 MLQIEFITDLGARVTVNVEHESRLLDVQRHYGRLGWTSGEIPSGGYQFPIENEADFDWSLIGARKWKSPEGEELVIHRGHAYRRIKYSRGAVSLAIFRGGKRQERYAVP 143
                                    10        20        30        40        50        60        70        80   ||  106||     134         
                                                                                                              84|   107|                 
                                                                                                              101    126                 


Chain E from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....eeeeee.hhhhhhhhhhhhhh............eeehhhhh...hhhhh.eeeee.....eeeee..eeeeeeee..ee....ee..eeeeee...eeeeee.....hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hqb E   0 TMLQIEFITDLGARVTVNVEHESRLLDVQRHYGRLGWTSGEIPSGGYQFPIENEADFDWSLIGARKWKSPEGEELVIHRGHAYRRRELEAVDSRKLKLPAAIKYSRGEYVSLAIFRGGKRQERYAVPG 144
                                     9        19        29        39        49        59        69        79        89        99      |126       136        
                                                                                                                                    106|                    
                                                                                                                                     124                    


Chain M from PDB  Type:DNA  Length:4
                                    
                 4hqb M   1 TTTT   4


Chain N from PDB  Type:DNA  Length:5
                                     
                 4hqb N   5 TTTTT   9
   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 4HQB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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 4hqb)
 
  Sites
(no "Sites" information available for 4hqb)
 
  Cis Peptide Bonds
    Arg A:93 - Lys A:94   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 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
  4hqb
    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
  DDRB_DEIRA | Q9RY80
    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
  DDRB_DEIRA | Q9RY80
    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
        DDRB_DEIRA | Q9RY80: 4noe

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4HQB)