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 PROTEIN YVYC FROM BACILLUS SUBTILIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR482.
 
Authors :  A. Eletsky, G. Liu, H. S. Atreya, D. K. Sukumaran, D. Wang, K. Cunningham, H. Janjua, L. -C. Ma, R. Xiao, J. Liu, M. Baran, T. B. Acton, B. Rost, G. T. Montelione, T. Szyperski, Northeast Structural Genomics Consortium (Nesg)
Date :  15 Jun 06  (Deposition) - 15 Aug 06  (Release) - 27 Oct 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nesg, Gft-Nmr, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Alpha-Beta, Flag, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Eletsky, D. K. Sukumaran, R. Xiao, T. B. Acton, B. Rost, G. T. Montelione, T. Szyperski
Nmr Structure Of Protein Yvyc From Bacillus Subtilis Reveals Unexpected Structural Similarity Between Two Pfam Families.
Proteins V. 76 1037 2009
PubMed-ID: 19455708  |  Reference-DOI: 10.1002/PROT.22459
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YVYC
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21
    Expression System StrainBL21(DE3)+MAGIC
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneYVYC
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    SynonymORF 99

 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 2HC5)

(-) Sites  (0, 0)

(no "Site" information available for 2HC5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HC5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HC5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HC5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HC5)

(-) Exons   (0, 0)

(no "Exon" information available for 2HC5)

(-) 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:117
 aligned with YVYC_BACSU | P39737 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:117
                                                                                                                                      109        
                                    10        20        30        40        50        60        70        80        90       100        |-       
           YVYC_BACSU     1 MNIERLTTLQPVWDRYDTQIHNQKDNDNEVPVHQVSYTNLAEMVGEMNKLLEPSQVHLKFELHDKLNEYYVKVIEDSTNEVIREIPPKRWLDFYAAMTEFLGLFVDEKK--------   -
               SCOP domains d2hc5a1 A:1-109 Hypothetical protein YvyC                                                                    -------- SCOP domains
               CATH domains -------2hc5A01 A:8-105 FlaG-like domain                                                                  ------------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh.....eeeeeeee..eeeeeeee.....eeeeehhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2hc5 A   1 LNIERLTTLQPVWDRYDTQIHNQKDNDNEVPVHQVSYTNLAEMVGEMNKLLEPSQVHLKFELHDKLNEYYVKVIEDSTNEVIREIPPKRWLDFYAAMTEFLGLFVDEKKLEHHHHHH 117
                                    10        20        30        40        50        60        70        80        90       100       110       

   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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HC5)

(-) Gene Ontology  (0, 0)

NMR Structure(hide GO term definitions)
    (no "Gene Ontology" information available for 2HC5)

 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 2hc5)
 
  Sites
(no "Sites" information available for 2hc5)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2hc5)
 

(-) 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
  2hc5
    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
  YVYC_BACSU | P39737
    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
  YVYC_BACSU | P39737
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2HC5)

(-) Related Entries Specified in the PDB File

7170 RELATED ID: SR482 RELATED DB: TARGETDB