1Y2QA

Crystal structure of the editing domain of threonyl-trna synthetase from pyrococcus abyssi
Total Genus 45
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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
45
sequence length
143
structure length
143
Chain Sequence
MRVLLIHSDYIEYEVKDKALKNPEPISEDMKRGRMEEVLVAFISVEKVDEKNPEEVSLKAIEEISKVAEQVKAENVFVYPFAHLSSELAKPSVAMDILNRVYQGLKERGFNVGKAPFGYYKAFKISCKGHPLAELSRTIVPEE
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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 Ligase
molecule keywords Threonyl-tRNA synthetase
publication title A D-amino acid editing module coupled to the translational apparatus in archaea
pubmed doi rcsb
source organism Pyrococcus abyssi
total genus 45
structure length 143
sequence length 143
ec nomenclature ec 6.1.1.3: Threonine--tRNA ligase.
pdb deposition date 2004-11-23

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF08915 tRNA-Thr_ED Archaea-specific editing domain of threonyl-tRNA synthetase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.50.80.10 Alpha Beta 3-Layer(bba) Sandwich D-tyrosyl-trna(Tyr) Deacylase; Chain: A; D-tyrosyl-trna(Tyr) Deacylase; Chain: A; 1y2qA01
1J7GA 4RRHA 4S03A 4RRJA 4S0LA 2HL0A 3LMUA 4RRMA 3KO4A 2HL2A 4RRIA 4RRFA 4RR9A 2HKZA 3KO3A 5J61A 4S02A 1Y2QA 3KO5A 4RRCA 1JKEA 3KNPA 4RR7A 3PD3A 3KOCA 4S0KA 2DBOA 3KOBA 4RR6A 4RRGA 4S0IA 4RRKA 3KNFA 4RRDA 4RRBA 4RRRA 4RRQA 3PD4A 4RR8A 2OKVA 4NBIA 3LMVA 3KO7A 3KODA 3PD2A 2HL1A 3PD5A 1TC5A 4RRAA 4RRLA 3LMTA 4S0JA 3KO9A 4NBJA
chains in the Genus database with same CATH superfamily
4RRHA 4S03A 3LMUA 3KO4A 4RRFA 3ZVTA 2Y59A 2Y4AA 5J61A 3ZVWA 5CEBA 2Y55A 3KOBA 4S0IA 2VGKA 4RRKA 2EX6A 4RRQA 2EXBA 3PD5A 4RRAA 3KO9A 2XDMA 1W5DA 1W8QA 2HL2A 4RRIA 3ZCZA 4RR9A 2HKZA 3KO3A 4S02A 1Y2QA 4RRCA 3PD3A 1W8YA 2EXAA 2J9PA 4RRBA 4RRRA 3PD4A 4RR8A 2OKVA 3LMVA 1W79A 4RRLA 1TC5A 3LMTA 4NBJA 5CEDA 5CECA 4RRMA 3KO5A 1JKEA 3KNPA 3KOCA 4S0KA 5CERA 2XK1A 2XLNA 3A3EA 4NBIA 4B4XA 3KODA 3A3DA 2HL1A 4B4ZA 2VGJA 1J7GA 2WKEA 2EX9A 4RRJA 4S0LA 2HL0A 3V39A 3A3IA 2EX2A 3A3FA 4RR7A 2DBOA 4RR6A 4RRGA 2EX8A 3KNFA 4RRDA 3KO7A 3PD2A 4BENA 4S0JA
chains in the Genus database with same CATH topology
4RRHA 4S03A 3LMUA 3KO4A 4RRFA 3ZVTA 2Y59A 2Y4AA 5J61A 3ZVWA 5CEBA 2Y55A 3KOBA 4S0IA 2VGKA 4RRKA 2EX6A 4RRQA 2EXBA 3PD5A 4RRAA 3KO9A 2XDMA 1W5DA 1W8QA 2HL2A 4RRIA 3ZCZA 4RR9A 2HKZA 3KO3A 4S02A 1Y2QA 4RRCA 3PD3A 1W8YA 2EXAA 2J9PA 4RRBA 4RRRA 3PD4A 4RR8A 2OKVA 3LMVA 1W79A 4RRLA 1TC5A 3LMTA 4NBJA 5CEDA 5CECA 4RRMA 3KO5A 1JKEA 3KNPA 3KOCA 4S0KA 5CERA 2XK1A 2XLNA 3A3EA 4NBIA 4B4XA 3KODA 3A3DA 2HL1A 4B4ZA 2VGJA 1J7GA 2WKEA 2EX9A 4RRJA 4S0LA 2HL0A 3V39A 3A3IA 2EX2A 3A3FA 4RR7A 2DBOA 4RR6A 4RRGA 2EX8A 3KNFA 4RRDA 3KO7A 3PD2A 4BENA 4S0JA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1J7G A;  4RRH A;  4S03 A;  4RRJ A;  4S0L A;  2HL0 A;  3LMU A;  4RRM A;  3KO4 A;  2HL2 A;  4RRI A;  4RRF A;  4RR9 A;  2HKZ A;  3KO3 A;  5J61 A;  4S02 A;  1Y2Q A;  3KO5 A;  4RRC A;  1JKE A;  3KNP A;  4RR7 A;  3PD3 A;  3KOC A;  4S0K A;  2DBO A;  3KOB A;  4RR6 A;  4RRG A;  4S0I A;  4RRK A;  3KNF A;  4RRD A;  4RRB A;  4RRR A;  4RRQ A;  3PD4 A;  4RR8 A;  2OKV A;  4NBI A;  3LMV A;  3KO7 A;  3KOD A;  3PD2 A;  2HL1 A;  3PD5 A;  1TC5 A;  4RRA A;  4RRL A;  3LMT A;  4S0J A;  3KO9 A;  4NBJ A; 
#chains in the Genus database with same CATH topology
 4RRH A;  4S03 A;  3LMU A;  3KO4 A;  4RRF A;  3ZVT A;  2Y59 A;  2Y4A A;  5J61 A;  3ZVW A;  5CEB A;  2Y55 A;  3KOB A;  4S0I A;  2VGK A;  4RRK A;  2EX6 A;  4RRQ A;  2EXB A;  3PD5 A;  4RRA A;  3KO9 A;  2XDM A;  1W5D A;  1W8Q A;  2HL2 A;  4RRI A;  3ZCZ A;  4RR9 A;  2HKZ A;  3KO3 A;  4S02 A;  1Y2Q A;  4RRC A;  3PD3 A;  1W8Y A;  2EXA A;  2J9P A;  4RRB A;  4RRR A;  3PD4 A;  4RR8 A;  2OKV A;  3LMV A;  1W79 A;  4RRL A;  1TC5 A;  3LMT A;  4NBJ A;  5CED A;  5CEC A;  4RRM A;  3KO5 A;  1JKE A;  3KNP A;  3KOC A;  4S0K A;  5CER A;  2XK1 A;  2XLN A;  3A3E A;  4NBI A;  4B4X A;  3KOD A;  3A3D A;  2HL1 A;  4B4Z A;  2VGJ A;  1J7G A;  2WKE A;  2EX9 A;  4RRJ A;  4S0L A;  2HL0 A;  3V39 A;  3A3I A;  2EX2 A;  3A3F A;  4RR7 A;  2DBO A;  4RR6 A;  4RRG A;  2EX8 A;  3KNF A;  4RRD A;  3KO7 A;  3PD2 A;  4BEN A;  4S0J A; 
#chains in the Genus database with same CATH homology
 4RRH A;  4S03 A;  3LMU A;  3KO4 A;  4RRF A;  3ZVT A;  2Y59 A;  2Y4A A;  5J61 A;  3ZVW A;  5CEB A;  2Y55 A;  3KOB A;  4S0I A;  2VGK A;  4RRK A;  2EX6 A;  4RRQ A;  2EXB A;  3PD5 A;  4RRA A;  3KO9 A;  2XDM A;  1W5D A;  1W8Q A;  2HL2 A;  4RRI A;  3ZCZ A;  4RR9 A;  2HKZ A;  3KO3 A;  4S02 A;  1Y2Q A;  4RRC A;  3PD3 A;  1W8Y A;  2EXA A;  2J9P A;  4RRB A;  4RRR A;  3PD4 A;  4RR8 A;  2OKV A;  3LMV A;  1W79 A;  4RRL A;  1TC5 A;  3LMT A;  4NBJ A;  5CED A;  5CEC A;  4RRM A;  3KO5 A;  1JKE A;  3KNP A;  3KOC A;  4S0K A;  5CER A;  2XK1 A;  2XLN A;  3A3E A;  4NBI A;  4B4X A;  3KOD A;  3A3D A;  2HL1 A;  4B4Z A;  2VGJ A;  1J7G A;  2WKE A;  2EX9 A;  4RRJ A;  4S0L A;  2HL0 A;  3V39 A;  3A3I A;  2EX2 A;  3A3F A;  4RR7 A;  2DBO A;  4RR6 A;  4RRG A;  2EX8 A;  3KNF A;  4RRD A;  3KO7 A;  3PD2 A;  4BEN A;  4S0J 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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