3RHU - JenaLib

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 :   12 Apr 11 (Deposition) - 09 Nov 11 (Release) - 18 Jan 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric 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
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Chain A from PDB  Type:PROTEIN  Length:141
 aligned with ALAXS_PYRHO | O58307 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
          ALAXS_PYRHO     2 YSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELL 151
               SCOP domains d3rhua_ A: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeee......hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.---------.eeeeee...eee.........hhhhh.eeeeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rhu A   2 YSIEVRTHSALHVVKGAVVKTAGSDAKWTTSTYVKGNKGVLIVKAALEPDKWGIAAIEALANEKVKENAPIKIYELPREEAEKMFGEDMYD---------ILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELL 151
                                    11        21        31        41        51        61        71        81        91|        -|      111       121       131       141       151
                                                                                                                     92       102

Chain B from PDB  Type:PROTEIN  Length:141
 aligned with ALAXS_PYRHO | O58307 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:150
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
          ALAXS_PYRHO     2 YSIEVRTHSALHVVKGAVVKVLGSEAKWTYSTYVKGNKGVLIVKFDRKPSDEEIREIERLANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELL 151
               SCOP domains d3rhub_ B: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh.hhhhhhhhhhhhhhhhhh.......ee..eeeeeee.....hhhhhhhhhhhhhhhhhh....eee..hhhhhhh........---------...eeee...eee........hhhhhh.eeeeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rhu B   2 YSIEVRTHSALHVVKGAVVKTAGSDAKWTTSTYVKGNKGVLIVKAALEPDKWGIAAIEALANEKVKENAPIKIYELPREEAEKMFGEDMYD---------ILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELL 151
                                    11        21        31        41        51        61        71        81        91|        -|      111       121       131       141       151
                                                                                                                     92       102

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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, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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