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 :  HYPOTHETICAL PROTEIN AT2G24940.1 FROM ARABIDOPSIS THALIANA HAS A CYTOCHROME B5 LIKE FOLD
 
Authors :  J. Song, D. A. Vinarov, E. M. Tyler, M. N. Shahan, R. C. Tyler, J. L. Markley, Center For Eukaryotic Structural Genomics (Cesg
Date :  08 Apr 04  (Deposition) - 13 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Structural Genomics, Hypothetical Protein, At2G24940. 1, Psi, Protein Structure Initiative, Center For Eukaryotic Structural Genomics, Cesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Song, D. A. Vinarov, E. M. Tyler, M. N. Shahan, R. C. Tyler, J. L. Markley
Hypothetical Protein At2G24940. 1 From Arabidopsis Thaliana Has A Cytochrome B5 Like Fold
J. Biomol. Nmr V. 30 215 2004
PubMed-ID: 15702529  |  Reference-DOI: 10.1023/B:JNMR.0000048943.34504.29
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME B5 DOMAIN-CONTAINING PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemCELL-FREE SYNTHESIS
    Expression System PlasmidPEU(N)HIS6
    Expression System Vector TypePLASMID
    GeneAT2G24940.1
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    Other DetailsWHEAT GERM CELL-FREE, IN VITRO EXPRESSION

 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 1T0G)

(-) Sites  (0, 0)

(no "Site" information available for 1T0G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T0G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1T0G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T0G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T0G)

(-) Exons   (0, 0)

(no "Exon" information available for 1T0G)

(-) 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:109
 aligned with SBP3_ARATH | Q9SK39 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:109
                                     1                                                                                                   
                                     1        11        21        31        41        51        61        71        81        91         
           SBP3_ARATH     - ---------MEFTAEQLSQYNGTDESKPIYVAIKGRVFDVTTGKSFYGSGGDYSMFAGKDASRALGKMSKNEEDVSPSLEGLTEKEINTLNDWETKFEAKYPVVGRVVS 100
               SCOP domains d1t0ga_ A: Putative steroid binding protein AT2G24940                                                         SCOP domains
               CATH domains 1t0gA00 A:1-109 Flavocytochrome B2, subunit A, domain 1                                                       CATH domains
               Pfam domains ----------Cyt-b5-1t0gA01 A:11-108                                                                           - Pfam domains
         Sec.struct. author .........eeeehhhhh...........eeee..eeee.hhhh..............eehhhhhhhh..............hhhhhhhhhhhhhhhhh...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1t0g A   1 MGHHHHHHLEEFTAEQLSQYNGTDESKPIYVAIKGRVFDVTTGKSFYGSGGDYSMFAGKDASRALGKMSKNEEDVSPSLEGLTEKEINTLNDWETKFEAKYPVVGRVVS 109
                                    10        20        30        40        50        60        70        80        90       100         

   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  (1, 1)

NMR Structure

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A   (SBP3_ARATH | Q9SK39)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0005496    steroid binding    Interacting selectively and non-covalently with a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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 1t0g)
 
  Sites
(no "Sites" information available for 1t0g)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1t0g)
 

(-) 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
  1t0g
    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
  SBP3_ARATH | Q9SK39
    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
  SBP3_ARATH | Q9SK39
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SBP3_ARATH | Q9SK391j03

(-) Related Entries Specified in the PDB File

6138 RELATED ID: GO.6705 RELATED DB: TARGETDB