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 :  RAP1/DNA COMPLEX
 
Authors :  Y. -V. Le Bihan, B. Matot, M. -H. Le Du
Date :  03 Aug 12  (Deposition) - 10 Apr 13  (Release) - 10 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Double-Myb, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. V. Le Bihan, B. Matot, O. Pietrement, M. J. Giraud-Panis, S. Gasparini, E. Le Cam, E. Gilson, B. Sclavi, S. Miron, M. H. Le Du
Effect Of Rap1 Binding On Dna Distortion And Potassium Permanganate Hypersensitivity.
Acta Crystallogr. , Sect. D V. 69 409 2013
PubMed-ID: 23519416  |  Reference-DOI: 10.1107/S0907444912049311
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA-BINDING PROTEIN RAP1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: 358-596
    Gene: RAP1, GRF1, TUF1, YNL216W, N1310
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: REPRESSOR/ACTIVATOR SITE-BINDING PROTEIN, SBF-E, TUF
 
Molecule 2 - TELOMERIC DNA
    Chains: C
    Engineered: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synthetic: YES
 
Molecule 3 - TELOMERIC DNA
    Chains: D
    Engineered: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (0, 0)

(no "Site" information available for 4GFB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:477 -Arg A:478
2Gly A:504 -Ser A:505
3Phe A:509 -Ala A:510
4Gly A:519 -Pro A:520

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GFB)

(-) 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:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh..hhhhhhhh......hhhhhhhhhhhhhhhhh..ee.................ee...........hhhhhhhhhhhhhhhhhhhhhh...............................hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gfb A 358 HNKASFTDEEDEFILDVVRKNPTRRTTHTLYDEISHYVPNHTGNSIRHRFRVYLSKRLEYVYEVDKFGKLVRDDDGNLIKTKVLPPSIKRKFSADEDYTLAIAVKKQFYRDLFQIDPDTGRSLITVPGSEPNFAAYRTQSRRGPIAREFFKHFAEEHAAHTENAWRDRFRKFLLAYGIDDYISYYEAEKAQNREPEPMKNLTNRPRPGVPTPGNYNSA 595
                                   367       377       387       397       407       417       427       437       447       457       467       477    || 506       516       526       536       546       556       566       576    || 587        
                                                                                                                                                      482|                                                                            581|            
                                                                                                                                                       502                                                                             583            


Chain C from PDB  Type:DNA  Length:29
                                                             
                 4gfb C   1 GTGTGAACCACACAACACCCACACACCAG  31
                                 || 12        22         
                                 6|                      
                                  9                      


Chain D from PDB  Type:DNA  Length:31
                                                               
                 4gfb D   1 ACCTGGTGTGTGGGTGTTGTGTGGTGTTCAC  31
                                    10        20        30
   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 4GFB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4gfb)
 
  Cis Peptide Bonds
    Gly A:477 - Arg A:478   [ RasMol ]  
    Gly A:504 - Ser A:505   [ RasMol ]  
    Gly A:519 - Pro A:520   [ RasMol ]  
    Phe A:509 - Ala A:510   [ 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
  4gfb
    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
  RAP1_YEAST | P11938
    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
  RAP1_YEAST | P11938
    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
        RAP1_YEAST | P11938: 1ign 2l42 3cz6 3owt 3ukg 4bj5 4bj6 4bjt

(-) Related Entries Specified in the PDB File

3ukg