3PD3A

Crystal structure of the editing domain of threonyl-trna synthetase from pyrococcus abyssi in complex with threonyl-3'-aminoadenosine
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
145
structure length
145
Chain Sequence
MRVLLIHSDYIEYEVKDKALKNPEPISEDMKRGRMEEVLVAFISVEKVDEKNPEEVSLKAIEEISKVAEQVKAENVFVYPFAHLSSELAKPSVAMDILNRVYQGLKERGFNVGKAPFGYYKAFKISCKGHPLAELSRTIVPEEAR
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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 Mechanistic insights into cognate substrate discrimination during proofreading in translation
pubmed doi rcsb
source organism Pyrococcus abyssi
total genus 46
structure length 145
sequence length 145
chains with identical sequence B
ec nomenclature ec 6.1.1.3: Threonine--tRNA ligase.
pdb deposition date 2010-10-22

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; 3pd3A01
3KOBA 2DBOA 3KO9A 3PD5A 4S02A 2HL1A 3KO3A 2HL0A 3KO4A 3LMVA 2HL2A 2OKVA 4RRCA 4S0LA 4NBIA 4RRQA 4S0KA 4RRDA 3KNPA 3KO7A 3PD2A 2HKZA 4RRRA 4NBJA 3KODA 4RR8A 4RR6A 4S0IA 3LMTA 4S03A 3KOCA 1TC5A 4RRFA 1J7GA 3KO5A 4RRGA 4RRJA 4RRBA 4RR7A 4RR9A 4S0JA 4RRAA 3KNFA 3PD3A 4RRMA 4RRIA 4RRHA 4RRKA 1Y2QA 1JKEA 3LMUA 3PD4A 4RRLA 5J61A
chains in the Genus database with same CATH superfamily
2DBOA 2Y4AA 2EXBA 2J9PA 3KO3A 2HL2A 3V39A 3KO7A 3PD2A 2HKZA 3KODA 4RR8A 4RR6A 2VGKA 1TC5A 5CEDA 2EX8A 1W79A 3KNFA 4RRIA 3LMUA 3PD4A 3A3DA 2Y55A 3KO9A 4BENA 4S02A 2HL1A 2HL0A 3LMVA 2OKVA 4RRCA 3A3IA 4NBIA 4RRQA 2EXAA 4RRDA 5CECA 4B4XA 4RRFA 4RRBA 4RR9A 4RRHA 5J61A 3PD5A 2XDMA 3A3FA 2XK1A 4S0LA 1W5DA 3KNPA 4NBJA 3ZCZA 4S0IA 3ZVWA 2Y59A 2EX9A 5CERA 1J7GA 3KO5A 4RRGA 4RRJA 4RR7A 4RRAA 3PD3A 1W8YA 3A3EA 1W8QA 3KOBA 2WKEA 2XLNA 3KO4A 4S0KA 4RRRA 4B4ZA 3LMTA 4S03A 3KOCA 3ZVTA 2VGJA 4S0JA 2EX6A 2EX2A 4RRMA 4RRKA 1JKEA 1Y2QA 4RRLA 5CEBA
chains in the Genus database with same CATH topology
2DBOA 2Y4AA 2EXBA 2J9PA 3KO3A 2HL2A 3V39A 3KO7A 3PD2A 2HKZA 3KODA 4RR8A 4RR6A 2VGKA 1TC5A 5CEDA 2EX8A 1W79A 3KNFA 4RRIA 3LMUA 3PD4A 3A3DA 2Y55A 3KO9A 4BENA 4S02A 2HL1A 2HL0A 3LMVA 2OKVA 4RRCA 3A3IA 4NBIA 4RRQA 2EXAA 4RRDA 5CECA 4B4XA 4RRFA 4RRBA 4RR9A 4RRHA 5J61A 3PD5A 2XDMA 3A3FA 2XK1A 4S0LA 1W5DA 3KNPA 4NBJA 3ZCZA 4S0IA 3ZVWA 2Y59A 2EX9A 5CERA 1J7GA 3KO5A 4RRGA 4RRJA 4RR7A 4RRAA 3PD3A 1W8YA 3A3EA 1W8QA 3KOBA 2WKEA 2XLNA 3KO4A 4S0KA 4RRRA 4B4ZA 3LMTA 4S03A 3KOCA 3ZVTA 2VGJA 4S0JA 2EX6A 2EX2A 4RRMA 4RRKA 1JKEA 1Y2QA 4RRLA 5CEBA
chains in the Genus database with same CATH homology


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

 
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#similar chains, but unknotted
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