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 NMR STRUCTURE OF THE Q251Q8_DESHY(21-82) PROTEIN FROM DESULFITOBACTERIUM HAFNIENSE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET DHR8C
 
Authors :  Y. Yang, T. A. Ramelot, J. R. Cort, H. Wang, C. Ciccosanti, E. L. Foote, M. H. Janjua, T. B. Acton, R. Xiao, J. K. Everett, G. T. Montelione, M. A. Ke Northeast Structural Genomics Consortium (Nesg)
Date :  23 Dec 09  (Deposition) - 12 Jan 10  (Release) - 13 Jul 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Yabp Family, Desulfitobacterium Hafniense, Structural Genomics, Psi- 2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yang, T. A. Ramelot, R. M. Mccarrick, S. Ni, E. A. Feldmann, J. R. Cort H. Wang, C. Ciccosanti, M. Jiang, H. Janjua, T. B. Acton, R. Xiao, J. K. Everett, G. T. Montelione, M. A. Kennedy
Combining Nmr And Epr Methods For Homodimer Protein Structure Determination.
J. Am. Chem. Soc. V. 132 11910 2010
PubMed-ID: 20698532  |  Reference-DOI: 10.1021/JA105080H

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) PMGK
    Expression System Taxid: 469008
    Expression System Vector: PET 21-23C
    Fragment: SEQUENCE DATABASE RESIDUES 20-82
    Gene: DSY0195
    Organism Scientific: DESULFITOBACTERIUM HAFNIENSE
    Organism Taxid: 138119
    Strain: Y51

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2KS0)

(-) Sites  (0, 0)

(no "Site" information available for 2KS0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KS0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KS0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KS0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2KS0)

(-) Exons   (0, 0)

(no "Exon" information available for 2KS0)

(-) 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:66
 aligned with Q251Q8_DESHY | Q251Q8 from UniProtKB/TrEMBL  Length:97

    Alignment length:71
                                    29        39        49        59        69        79        89 
          Q251Q8_DESHY   20 MDNRQFLSLTGVSKVQSFDPKEILLETIQGVLSIKGEKLGIKHLDLKAGQVEVEGLIDALVYPRNSGSRQN 90
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..eeeeeee...eeeeee..eeeeeeeeeee-----.....eeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  2ks0 A  1 MDNRQFLSLTGVSKVQSFDPKEILLETIQGVLSIKGEKLG-----LKAGQVEVEGLIDALVYPLEHHHHHH 71
                                    10        20        30        40     |  50        60        70 
                                                                  40    46                         


Chain B from PDB  Type:PROTEIN  Length:66
 aligned with Q251Q8_DESHY | Q251Q8 from UniProtKB/TrEMBL  Length:97

    Alignment length:71
                                    29        39        49        59        69        79        89 
          Q251Q8_DESHY   20 MDNRQFLSLTGVSKVQSFDPKEILLETIQGVLSIKGEKLGIKHLDLKAGQVEVEGLIDALVYPRNSGSRQN 90
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
           Pfam domains (1) YabP-2ks0B01 B:1-63                                            -------- Pfam domains (1)
           Pfam domains (2) YabP-2ks0B02 B:1-63                                            -------- Pfam domains (2)
         Sec.struct. author ....eeeee....eeeeee..eeeeee..eeeeeeeeeee-----.....eeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  2ks0 B  1 MDNRQFLSLTGVSKVQSFDPKEILLETIQGVLSIKGEKLG-----LKAGQVEVEGLIDALVYPLEHHHHHH 71
                                    10        20        30        40     |  50        60        70 
                                                                  40    46
   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 2KS0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KS0)

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: no clan defined [family: YabP] (2)

(-) Gene Ontology  (0, 0)

NMR Structure(hide GO term definitions)
    (no "Gene Ontology" information available for 2KS0)

 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 2ks0)
 
  Sites
(no "Sites" information available for 2ks0)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ks0)
 

(-) 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
  2ks0
    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
  Q251Q8_DESHY | Q251Q8
    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
  Q251Q8_DESHY | Q251Q8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q251Q8_DESHY | Q251Q8: 2kyi 3ipf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2KS0)