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 A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM OCHROBACTRUM ANTHROPI (OANT_4429), TARGET EFI-510151, C-TERMIUS BOUND IN LIGAND BINDING POCKET
 
Authors :  M. W. Vetting, N. F. Al Obaidi, L. L. Morisco, S. R. Wasserman, M. Stead, J. D. Attonito, A. Scott Glenn, S. Chowdhury, B. Evans, B. Hillerich, R. D. Seidel, K. L. Whalen, J. A. Gerlt, S. C. Almo, Enzyme Function In (Efi)
Date :  12 Mar 14  (Deposition) - 23 Apr 14  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Trap Periplasmic Solute Binding Family, Enzyme Function Initiative, Efi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Vetting, N. Al-Obaidi, S. Zhao, B. San Francisco, J. Kim, D. J. Wichelecki, J. T. Bouvier, J. O. Solbiati, H. Vu, X. Zhang, D. A. Rodionov, J. D. Love, B. S. Hillerich, R. D. Seidel, R. J. Quinn, A. L. Osterman, J. E. Cronan, M. P. Jacobson, J. A. Gerlt, S. C. Almo
Experimental Strategies For Functional Annotation And Metabolism Discovery: Targeted Screening Of Solute Binding Proteins And Unbiased Panning Of Metabolomes.
Biochemistry V. 54 909 2015
PubMed-ID: 25540822  |  Reference-DOI: 10.1021/BI501388Y

(-) Compounds

Molecule 1 - TRAP DICARBOXYLATE TRANSPORTER, DCTP SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: OANT_4429
    Organism Scientific: OCHROBACTRUM ANTHROPI
    Organism Taxid: 439375
    Strain: ATCC 49188
    Synonym: TRAP PERIPLASMIC SOLUTE BINDING PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4P47)

(-) Sites  (0, 0)

(no "Site" information available for 4P47)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P47)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4P47)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P47)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P47)

(-) Exons   (0, 0)

(no "Exon" information available for 4P47)

(-) 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:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee......hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeeee......hhhhhh..eee...hhhhhhhhhhh..eee..hhhhhhhhhhhh...eeee.hhhhhhhhhhhh..eeeeeeeeeeeeeeeeehhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p47 A  26 EIRSQTIKFAAANSKGHPQVTGMEKFAELVKEKSGGQINVKLFPGGVLGSDPQTLSGLQGGVVEMTVMNAGILSSTVKAFEAVDLPFLFNSGEEADKVMDGPFGTNLMKRLPDTGLIGLAYWELGFRNLTNNRHPVAKLEDIAGLKIRTLQSPVPVALFNALGANAVPLPYTELYTALETGTVDGQENPNANIINAKFYEVQKYLTLTRHQYNPQIVMISKKFWDRLNDEEKAVIEQAAVEARDYQRKVSREQDATALDEIKKTGMQVTELTPEETTRLRDAVKPIIDKFTAEIGAETVDELFAELKKVRGENAENLYFQ 345
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345
   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 4P47)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P47)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P47)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

 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 4p47)
 
  Sites
(no "Sites" information available for 4p47)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4p47)
 

(-) 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
  4p47
    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
  A6X7C5_OCHA4 | A6X7C5
    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
  A6X7C5_OCHA4 | A6X7C5
    Protein Disorder Prediction: DisEMBL | 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 4P47)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4P47)