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(-) Description

Title :  EPITOPE BACKBONE GRAFTING BY COMPUTATIONAL DESIGN FOR IMPROVED PRESENTATION OF LINEAR EPITOPES ON SCAFFOLD PROTEINS
 
Authors :  M. L. Azoitei, Y. A. Ban, J. P. Julien, S. Bryson, A. Schroeter, O. Kalyuz J. R. Porter, Y. Adachi, D. Baker, E. Szabo, E. F. Pai, W. R. Schief
Date :  06 Apr 11  (Deposition) - 09 Nov 11  (Release) - 18 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Grafting, Flexible Backbone Design, Epitope-Scaffold, Hiv, Immunogen Design, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Azoitei, Y. E. Ban, J. P. Julien, S. Bryson, A. Schroeter, O. Kalyuzhniy, J. R. Porter, Y. Adachi, D. Baker, E. F. Pai, W. R. Schief
Computational Design Of High-Affinity Epitope Scaffolds By Backbone Grafting Of A Linear Epitope.
J. Mol. Biol. V. 415 175 2012
PubMed-ID: 22061265  |  Reference-DOI: 10.1016/J.JMB.2011.10.003

(-) Compounds

Molecule 1 - BB_1WNU_001
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SEE REMARK 999
    Gene: ALAXS, PH0574
    Mutation: YES
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:9 , HIS A:13 , CYS A:116 , HIS A:120BINDING SITE FOR RESIDUE ZN A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RFN)

(-) 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:151
 aligned with ALAXS_PYRHO | O58307 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:151
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151 
          ALAXS_PYRHO     2 YSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLE 152
               SCOP domains d3rfna_ A: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee..eeeeeee.......hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhh..........eeeeeee...eeee.......hhhhhh..eeeeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rfn A   2 YSIEVRTHSALHVVKGAVVKAAGSAAKWTTSTYVKGNKGVLIVKAALELDKWAWAAMEALANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLE 152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
   Legend:   → Mismatch (orange background)
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  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)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ALAXS_PYRHO | O58307)
molecular function
    GO:0002161    aminoacyl-tRNA editing activity    The hydrolysis of an incorrectly aminoacylated tRNA.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0006450    regulation of translational fidelity    Any process that modulates the ability of the translational apparatus to interpret the genetic code.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  ALAXS_PYRHO | O58307
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 Related Entries

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

UniProtKB/Swiss-Prot
        ALAXS_PYRHO | O58307: 1v4p 1v7o 1wnu 1wxo 3rhu

(-) Related Entries Specified in the PDB File

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