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

(-) Description

Title :  SOLUTION STRUCTURE OF THE HMG BOX DOMAIN FROM HUMAN WD REPEAT AND HMG-BOX DNA BINDING PROTEIN 1
 
Authors :  T. Tomizawa, T. Kigawa, K. Saito, S. Koshiba, M. Inoue, Y. O. Kamatari, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  24 Nov 05  (Deposition) - 24 May 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  High Mobility Group Box Domain, Helix-Turn-Helix, Dna Binding, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Gene Regulation, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Tomizawa, T. Kigawa, K. Saito, S. Koshiba, M. Inoue, Y. O. Kamatari, S. Yokoyama
Solution Structure Of The Hmg Box Domain From Human Wd Repeat And Hmg-Box Dna Binding Protein 1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - WD REPEAT AND HMG-BOX DNA BINDING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression System PlasmidP050111-08
    Expression System Vector TypePLASMID
    FragmentHMG BOX DOMAIN
    GeneWDHD1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymACIDIC NUCLEOPLASMIC DNA- BINDING PROTEIN 1, AND- 1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2D7L)

(-) Sites  (0, 0)

(no "Site" information available for 2D7L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D7L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D7L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D7L)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.WDHD1_HUMAN1015-1084  1A:8-75

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003605861cENSE00001890909chr14:55493795-5549374650WDHD1_HUMAN-00--
1.1eENST000003605861eENSE00002195219chr14:55493521-5549342993WDHD1_HUMAN1-26260--
1.2ENST000003605862ENSE00001606792chr14:55480314-55480203112WDHD1_HUMAN26-63380--
1.3ENST000003605863ENSE00001770131chr14:55477178-55477027152WDHD1_HUMAN64-114510--
1.4ENST000003605864ENSE00001740647chr14:55475437-55475326112WDHD1_HUMAN114-151380--
1.5ENST000003605865ENSE00002157060chr14:55475084-5547503451WDHD1_HUMAN152-168170--
1.6ENST000003605866ENSE00000572360chr14:55474093-5547399896WDHD1_HUMAN169-200320--
1.7ENST000003605867ENSE00000657700chr14:55468903-5546881193WDHD1_HUMAN201-231310--
1.8ENST000003605868ENSE00002152866chr14:55467710-55467604107WDHD1_HUMAN232-267360--
1.9ENST000003605869ENSE00000657696chr14:55467362-55467221142WDHD1_HUMAN267-314480--
1.10ENST0000036058610ENSE00000657694chr14:55462531-55462321211WDHD1_HUMAN315-385710--
1.11ENST0000036058611ENSE00000657692chr14:55458118-55457931188WDHD1_HUMAN385-447630--
1.12ENST0000036058612ENSE00000657691chr14:55455930-55455746185WDHD1_HUMAN448-509620--
1.13ENST0000036058613ENSE00000657689chr14:55454105-55453864242WDHD1_HUMAN509-590820--
1.14ENST0000036058614ENSE00001388096chr14:55451578-55451441138WDHD1_HUMAN590-636470--
1.15ENST0000036058615ENSE00000657685chr14:55448414-55448258157WDHD1_HUMAN636-688530--
1.16ENST0000036058616ENSE00000657683chr14:55434112-55433998115WDHD1_HUMAN688-726390--
1.17ENST0000036058617ENSE00000657681chr14:55433324-55433193132WDHD1_HUMAN727-770440--
1.18ENST0000036058618ENSE00000657679chr14:55429890-55429670221WDHD1_HUMAN771-844740--
1.19ENST0000036058619ENSE00000657677chr14:55429571-55429456116WDHD1_HUMAN844-883400--
1.20ENST0000036058620ENSE00000657675chr14:55429269-5542921654WDHD1_HUMAN883-901190--
1.21ENST0000036058621ENSE00000657673chr14:55424353-5542431044WDHD1_HUMAN901-915150--
1.22ENST0000036058622ENSE00000657671chr14:55423922-55423752171WDHD1_HUMAN916-972570--
1.23ENST0000036058623ENSE00000657669chr14:55422412-55422279134WDHD1_HUMAN973-1017451A:1-8 (gaps)45
1.24bENST0000036058624bENSE00000657667chr14:55411188-55411050139WDHD1_HUMAN1017-1063471A:8-5447
1.25dENST0000036058625dENSE00001907538chr14:55408408-554056682741WDHD1_HUMAN1064-1129661A:55-81 (gaps)32

(-) 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:81
 aligned with WDHD1_HUMAN | O75717 from UniProtKB/Swiss-Prot  Length:1129

    Alignment length:123
                                   982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092   
         WDHD1_HUMAN    973 ASAASYFQKRNSQTNKTEEVKEENLKNVLSETPAICPPQNTENQRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGETASEGTEAKKRKRVVDESDETEN 1095
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....-------------------------------------.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhh..........hhhhh-----...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------HMG_BOX_2  PDB: A:8-75 UniProt: 1015-1084                             ----------- PROSITE
           Transcript 1 (1) Exon 1.23  PDB: A:1-8 (gaps)                 ----------------------------------------------Exon 1.25d  PDB: A:55-81 (gaps)  Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.24b  PDB: A:8-54 UniProt: 1017-1063     -------------------------------- Transcript 1 (2)
                2d7l A    1 GSSGS-------------------------------------SGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGETASEGTEAKKRK-----SGPSSG   81
                                |    -         -         -         -  |     13        23        33        43        53        63        73 |     |78   
                                5                                     6                                                                   75    76     

   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 2D7L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D7L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D7L)

(-) Gene Ontology  (5, 5)

NMR Structure(hide GO term definitions)
Chain A   (WDHD1_HUMAN | O75717)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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 2d7l)
 
  Sites
(no "Sites" information available for 2d7l)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2d7l)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2d7l
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  WDHD1_HUMAN | O75717
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  WDHD1_HUMAN | O75717
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        WDHD1_HUMAN | O757175gva 5gvb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2D7L)