3RFNA

Epitope backbone grafting by computational design for improved presentation of linear epitopes on scaffold proteins
Total Genus 46
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
46
sequence length
151
structure length
151
Chain Sequence
YSIEVRTHSALHVVKGAVVKAAGSAAKWTTSTYVKGNKGVLIVKAALELDKWAWAAMEALANEKVKENAPIKIYELPREEAEKMFGEDMYDLFPVPEDVRILKVVVIEDWNVNACNKEHTKTTGEIGPIKIRKVRFRKSKGLLEIHFELLE
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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molecule tags De novo protein
molecule keywords BB_1wnu_001
publication title Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope.
pubmed doi rcsb
source organism Pyrococcus horikoshii
total genus 46
structure length 151
sequence length 151
ec nomenclature
pdb deposition date 2011-04-06
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.30.54.20 Alpha Beta 2-Layer Sandwich Replication Terminator Protein; Chain A, domain 2 Replication Terminator Protein; Chain A, domain 2 3rfnA02
3.30.980.10 Alpha Beta 2-Layer Sandwich Threonyl-tRNA Synthetase; Chain A, domain 2 Threonyl-trna Synthetase; Chain A, domain 2 3rfnA01
1V7OA 2ZZEA 1NYRA 1TKGA 3RFNA 2ZZGA 1V4PA 1NYQA 1TKYA 1WXOA 2ZTGA 1WNUA 1TKEA 3KEWA 1TJEA 3RHUA 2ZZFA 1QF6A 3WQZA 2E1BA
chains in the Genus database with same CATH superfamily
3I7KA 4CI1A 1V4PA 2IUUA 3I7PA 3ZWDA 2EWJA 2ZTGA 2Y6IA 4XR0A 3ZX5A 3KEWA 4E54A 4A0AA 3RHUA 1XVIA 3ZX4A 3I7OA 4E5ZA 5FQDA 1ECRA 3WQZA 4AREA 2ZZEA 3ZW7A 4CI2A 3RFNA 2B5LA 3EI1A 2B5MA 2Y50A 3I8CA 1WXOA 4ARFA 3ZU6A 3EI2A 3ZTWA 1TJEA 1QF6A 2ZOSA 3ZWKA 3I7LA 4XR1A 1NYRA 2I06A 4A0BA 2I05A 4CI3A 4AR8A 4XR2A 1NYQA 4A09A 3I7HA 3EI4A 3I89A 4TZ4A 3ZUPA 1V7OA 1TKGA 2ZZGA 3EI3A 4A11A 1WZCA 2HYEA 3I8EA 1TKYA 2IUSA 3I7NA 2Y3UA 4AR9A 1WNUA 1TKEA 2ZZFA 2IUTA 4A08A 3E0CA 4AR1A 4XR3A 3ZTYA 2E1BA
chains in the Genus database with same CATH topology
1V7OA 2ZZEA 4XR1A 1NYRA 3I7KA 4CI2A 1TKGA 4CI1A 3RFNA 2ZZGA 2I06A 2B5LA 4A0BA 1V4PA 2I05A 2IUUA 3EI1A 3EI3A 4A11A 3I7PA 4CI3A 2HYEA 2B5MA 2Y50A 4AR8A 2EWJA 4XR2A 3I8CA 1NYQA 3I8EA 1TKYA 1WXOA 2ZTGA 2Y6IA 4XR0A 4ARFA 2IUSA 3I7NA 2Y3UA 4AR9A 4A09A 1WNUA 1TKEA 3KEWA 3I7HA 4A0AA 3EI2A 3EI4A 4E54A 1TJEA 5FQDA 3RHUA 2ZZFA 2IUTA 4A08A 3E0CA 4AR1A 4XR3A 1QF6A 3I7OA 4E5ZA 3I89A 1ECRA 3WQZA 3I7LA 4AREA 2E1BA 4TZ4A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1V7O A;  2ZZE A;  1NYR A;  1TKG A;  3RFN A;  2ZZG A;  1V4P A;  1NYQ A;  1TKY A;  1WXO A;  2ZTG A;  1WNU A;  1TKE A;  3KEW A;  1TJE A;  3RHU A;  2ZZF A;  1QF6 A;  3WQZ A;  2E1B A; 
#chains in the Genus database with same CATH topology
 3I7K A;  4CI1 A;  1V4P A;  2IUU A;  3I7P A;  3ZWD A;  2EWJ A;  2ZTG A;  2Y6I A;  4XR0 A;  3ZX5 A;  3KEW A;  4E54 A;  4A0A A;  3RHU A;  1XVI A;  3ZX4 A;  3I7O A;  4E5Z A;  5FQD A;  1ECR A;  3WQZ A;  4ARE A;  2ZZE A;  3ZW7 A;  4CI2 A;  3RFN A;  2B5L A;  3EI1 A;  2B5M A;  2Y50 A;  3I8C A;  1WXO A;  4ARF A;  3ZU6 A;  3EI2 A;  3ZTW A;  1TJE A;  1QF6 A;  2ZOS A;  3ZWK A;  3I7L A;  4XR1 A;  1NYR A;  2I06 A;  4A0B A;  2I05 A;  4CI3 A;  4AR8 A;  4XR2 A;  1NYQ A;  4A09 A;  3I7H A;  3EI4 A;  3I89 A;  4TZ4 A;  3ZUP A;  1V7O A;  1TKG A;  2ZZG A;  3EI3 A;  4A11 A;  1WZC A;  2HYE A;  3I8E A;  1TKY A;  2IUS A;  3I7N A;  2Y3U A;  4AR9 A;  1WNU A;  1TKE A;  2ZZF A;  2IUT A;  4A08 A;  3E0C A;  4AR1 A;  4XR3 A;  3ZTY A;  2E1B A; 
#chains in the Genus database with same CATH homology
 1V7O A;  2ZZE A;  4XR1 A;  1NYR A;  3I7K A;  4CI2 A;  1TKG A;  4CI1 A;  3RFN A;  2ZZG A;  2I06 A;  2B5L A;  4A0B A;  1V4P A;  2I05 A;  2IUU A;  3EI1 A;  3EI3 A;  4A11 A;  3I7P A;  4CI3 A;  2HYE A;  2B5M A;  2Y50 A;  4AR8 A;  2EWJ A;  4XR2 A;  3I8C A;  1NYQ A;  3I8E A;  1TKY A;  1WXO A;  2ZTG A;  2Y6I A;  4XR0 A;  4ARF A;  2IUS A;  3I7N A;  2Y3U A;  4AR9 A;  4A09 A;  1WNU A;  1TKE A;  3KEW A;  3I7H A;  4A0A A;  3EI2 A;  3EI4 A;  4E54 A;  1TJE A;  5FQD A;  3RHU A;  2ZZF A;  2IUT A;  4A08 A;  3E0C A;  4AR1 A;  4XR3 A;  1QF6 A;  3I7O A;  4E5Z A;  3I89 A;  1ECR A;  3WQZ A;  3I7L A;  4ARE A;  2E1B A;  4TZ4 A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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