Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT NITROBINDIN M75L/H76L/Q96C/V128W/M148L/H158L (NB9) FROM ARABIDOPSIS THALIANA
 
Authors :  E. Mizohata, K. Fukumoto, A. Onoda, M. Bocola, M. Arlt, T. Inoue, U. Schw T. Hayashi
Date :  08 Oct 13  (Deposition) - 02 Apr 14  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Barrel, Intracellular Transport, Hydrophobic Ligands, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Fukumoto, A. Onoda, E. Mizohata, M. Bocola, T. Inoue, U. Schwaneberg, T. Hayashi
A Rhodium Complex-Linked Hybrid Biocatalyst: Stereo-Controlled Phenylacetylene Polymerization Within An Engineered Protein Cavity
Chemcatchem 2014
PubMed: search  |  Reference-DOI: 10.1002/CCTC.201301055

(-) Compounds

Molecule 1 - UPF0678 FATTY ACID-BINDING PROTEIN-LIKE PROTEIN AT1G79260
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET42B(+)
    Expression System Strain: BL21STAR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AT1G79260, AT1G79260.1, YUP8H12R.14
    Mutation: YES
    Organism Common: MOUSE-EAR CRESS, THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: NITROBINDIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3WJF)

(-) Sites  (0, 0)

(no "Site" information available for 3WJF)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WJF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WJF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WJF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WJF)

(-) Exons   (0, 0)

(no "Exon" information available for 3WJF)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:153
 aligned with Y1926_ARATH | O64527 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:153
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163   
          Y1926_ARATH    14 PPVHPFVAPLSYLLGTWRGQGEGEYPTIPSFRYGEEIRFSHSGKPVIAYTQKTWKLESGAPMHAESGYFRPRPDGSIEVVIAQSTGLVEVQKGTYNVDEQSIKLKSDLVGNASKVKEISREFELVDGKLSYVVRMSTTTNPLQPHLKAILDKL 166
               SCOP domains d3wjfa_ A: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhheeeeeeeee.......eeeeeeeeee......eeeeeeee......eeeeeeeeeee....eeeeeeee....eeeeeeeee....eeeeeeeeee....eeeeeeeeeee..eeeeeeeeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wjf A  14 PPVHPFVAPLSYLLGTWRGQGEGEYPTIPSFRYGEEIRFSHSGKPVIAYTQKTWKLESGAPLLAESGYFRPRPDGSIEVVIACSTGLVEVQKGTYNVDEQSIKLKSDLVGNASKWKEISREFELVDGKLSYVVRLSTTTNPLQPLLKAILDKL 166
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163   


Chain B from PDB  Type:PROTEIN  Length:153
 aligned with Y1926_ARATH | O64527 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:153
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163   
          Y1926_ARATH    14 PPVHPFVAPLSYLLGTWRGQGEGEYPTIPSFRYGEEIRFSHSGKPVIAYTQKTWKLESGAPMHAESGYFRPRPDGSIEVVIAQSTGLVEVQKGTYNVDEQSIKLKSDLVGNASKVKEISREFELVDGKLSYVVRMSTTTNPLQPHLKAILDKL 166
               SCOP domains d3wjfb_ B: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhheeeeeeeee.......eeeeeeeeee......eeeeeeeee.....eeeeeeeeeee....eeeeeeee....eeeeeeeee....eeeeeeeeee....eeeeeeeeeee..eeeeeeeeee.....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wjf B  14 PPVHPFVAPLSYLLGTWRGQGEGEYPTIPSFRYGEEIRFSHSGKPVIAYTQKTWKLESGAPLLAESGYFRPRPDGSIEVVIACSTGLVEVQKGTYNVDEQSIKLKSDLVGNASKWKEISREFELVDGKLSYVVRLSTTTNPLQPLLKAILDKL 166
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WJF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WJF)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Y1926_ARATH | O64527)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  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 3wjf)
 
  Sites
(no "Sites" information available for 3wjf)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3wjf)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  3wjf
    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
  Y1926_ARATH | O64527
    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
  Y1926_ARATH | O64527
    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
        Y1926_ARATH | O64527: 2a13 2q4n 3emm 3wjb 3wjc 3wjd 3wje 3wjg 4ymy

(-) Related Entries Specified in the PDB File

3wjb 3wjc 3wjd 3wje 3wjg