Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  RECOGNITION DYNAMICS UP TO MICROSECONDS REVEALED FROM RDC DERIVED UBIQUITIN ENSEMBLE IN SOLUTION
 
Authors :  O. F. Lange, N. A. Lakomek, C. Fares, G. Schroder, K. Walter, S. Becker, J. Meiler, H. Grubmuller, C. Griesinger, B. L. De Groot
Date :  25 Apr 08  (Deposition) - 24 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (116x)
Keywords :  Ubiquitin, Rdc, Residual Dipolar Coupling, , Cytoplasm, Nucleus, Ubl Conjugation, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. F. Lange, N. A. Lakomek, C. Fares, G. F. Schroder, K. F. Walter, S. Becker, J. Meiler, H. Grubmuller, C. Griesinger, B. L. De Groot
Recognition Dynamics Up To Microseconds Revealed From An Rdc-Derived Ubiquitin Ensemble In Solution.
Science V. 320 1471 2008
PubMed-ID: 18556554  |  Reference-DOI: 10.1126/SCIENCE.1157092
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS

 Structural Features

(-) Chains, Units

  
NMR Structure (116x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2K39)

(-) Sites  (0, 0)

(no "Site" information available for 2K39)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K39)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2K39)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2K39)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.UBIQP_XENLA16-91
92-167		  1-
A:1-76
2UBIQUITIN_1PS00299 Ubiquitin domain signature.UBIQP_XENLA42-67
118-143		  1-
A:27-52

(-) Exons   (0, 0)

(no "Exon" information available for 2K39)

(-) Sequences/Alignments

NMR Structure
   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:76
 aligned with UBIQP_XENLA | P62972 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:76
                                   101       111       121       131       141       151       161      
          UBIQP_XENLA    92 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 167
               SCOP domains d2k39a_ A: Ubiquitin                                                         SCOP domains
               CATH domains 2k39A00 A:1-76                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhh......eeeee..ee................eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: A:1-76 UniProt: 92-167                                     PROSITE (1)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: A:27-52 ------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------- Transcript
                 2k39 A   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                    10        20        30        40        50        60        70
   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, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2K39)

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain A   (UBIQP_XENLA | P62972)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 Visualization

(-) Interactive Views

NMR Structure
  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 2k39)
 
  Sites
(no "Sites" information available for 2k39)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2k39)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  2k39
    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
  UBIQP_XENLA | P62972
    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
  UBIQP_XENLA | P62972
    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
        UBIQP_XENLA | P62972: 1cmx 1gjz 1ud7 1uzx 2kde

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2K39)