4CNEB

Crystal structure of e.coli trmj in complex with s-adenosyl-l- homocysteine
Warning
  • Chain breaks within knot 31 (displayed as a gray area on the plot and as '-' on the sequence). The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Knot K +31

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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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+31 84-136 53 1-83, 137-170 83 34 knot
Chain Sequence
DPALRALQNIRIVLVETSHTGNMGSVARAMKTMGLTNLWLVNPLVKPDSQAIALAAGASDVIGNAHIVDTLDEALAGCSLVVGTSA-----PWPMLDPRECGLKSVAEAANTPVALVFGRERVGLTNEELQKCHYHVAIAANPEYSSLNLAMAVQVIAYEVRMAWLATQ
Whole chain analysis

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Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1


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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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3.1 82-132 51 1-81, 133-164 81 32 knot
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2.1 72-129 58 1-71 135-164 130-134 71 30 slipknot
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3.1 85-143 59 1-81, 162-164 82-84, 144-161 81 3 slipknot
sequence length 169
structure length 164
publication title Characterization of Two Homologous 2'-O-Methyltransferases Showing Different Specificities for Their tRNA Substrates.
pubmed doi rcsb
molecule tags Transferase
molecule keywords TRNA (CYTIDINE/URIDINE-2'-O-)-METHYLTRANSFERASE TRMJ
source organism Escherichia coli
missing residues 87-91
ec nomenclature ec 2.1.1.200: tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase.
pdb deposition date 2014-01-22
KnotProt deposition date 2018-09-16

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
B PF00588 SpoU_methylase SpoU rRNA Methylase family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4cneB01
3ILKA 2O3AA 3AIAA 3L8UA 1P9PA 3GYQA 2QWVA 3KY7A 1X7OA 3KTYA 3ONPA 1X7PA 3DCMX 3E5YA 1MXIA 2QMMA 2I6DA 4H3ZA 4H3YA 2Z0YA 1K3RA 1NXZA 3NK7A 1V6ZA 3AI9X 1UAMA 1VHKA 1GZ0A 1VHYA 1ZJRA 4CNFB 3AXZA 3QUVA 4IG6A 1UAJA 1V2XA 2HA8A 3NK6A 4FAKA 2YY8A 1O6DA 3IC6A 1J85A 4CNEB 3IEFA 2CX8A 3KNUA 4E8BA 1TO0A 1UALA 3N4JA 1NS5A 1UAKA 1VH0A 3N4KA 4CNGB
chains in the KnotProt database with same CATH superfamily
3ILKA 2O3AA 3AIAA 3L8UA 1P9PA 3GYQA 2QWVA 3KY7A 1X7OA 3KTYA 3ONPA 1X7PA 3DCMX 3E5YA 1MXIA 2QMMA 2I6DA 4H3ZA 4H3YA 2Z0YA 1K3RA 1NXZA 3NK7A 1V6ZA 3AI9X 1UAMA 1VHKA 1GZ0A 1VHYA 1ZJRA 4CNFB 3AXZA 3QUVA 4IG6A 1UAJA 1V2XA 2HA8A 3NK6A 4FAKA 2YY8A 1O6DA 3IC6A 1J85A 4CNEB 3IEFA 2CX8A 3KNUA 4E8BA 1TO0A 1UALA 3N4JA 1NS5A 1UAKA 1VH0A 3N4KA 4CNGB
chains in the KnotProt database with same CATH topology
3ILKA 2O3AA 3AIAA 3L8UA 1P9PA 3GYQA 2QWVA 3KY7A 1X7OA 3KTYA 3ONPA 1X7PA 3DCMX 3E5YA 1MXIA 2QMMA 2I6DA 4H3ZA 4H3YA 2Z0YA 1K3RA 1NXZA 3NK7A 1V6ZA 3AI9X 1UAMA 1VHKA 1GZ0A 1VHYA 1ZJRA 4CNFB 3AXZA 3QUVA 4IG6A 1UAJA 1V2XA 2HA8A 3NK6A 4FAKA 2YY8A 1O6DA 3IC6A 1J85A 4CNEB 3IEFA 2CX8A 3KNUA 4E8BA 1TO0A 1UALA 3N4JA 1NS5A 1UAKA 1VH0A 3N4KA 4CNGB
chains in the KnotProt database with same CATH homology

  
#chains in the KnotProt database with same CATH superfamily
 3ILK A;  2O3A A;  3AIA A;  3L8U A;  1P9P A;  3GYQ A;  2QWV A;  3KY7 A;  1X7O A;  3KTY A;  3ONP A;  1X7P A;  3DCM X;  3E5Y A;  1MXI A;  2QMM A;  2I6D A;  4H3Z A;  4H3Y A;  2Z0Y A;  1K3R A;  1NXZ A;  3NK7 A;  1V6Z A;  3AI9 X;  1UAM A;  1VHK A;  1GZ0 A;  1VHY A;  1ZJR A;  4CNF B;  3AXZ A;  3QUV A;  4IG6 A;  1UAJ A;  1V2X A;  2HA8 A;  3NK6 A;  4FAK A;  2YY8 A;  1O6D A;  3IC6 A;  1J85 A;  4CNE B;  3IEF A;  2CX8 A;  3KNU A;  4E8B A;  1TO0 A;  1UAL A;  3N4J A;  1NS5 A;  1UAK A;  1VH0 A;  3N4K A;  4CNG B; 
#chains in the KnotProt database with same CATH topology
 3ILK A;  2O3A A;  3AIA A;  3L8U A;  1P9P A;  3GYQ A;  2QWV A;  3KY7 A;  1X7O A;  3KTY A;  3ONP A;  1X7P A;  3DCM X;  3E5Y A;  1MXI A;  2QMM A;  2I6D A;  4H3Z A;  4H3Y A;  2Z0Y A;  1K3R A;  1NXZ A;  3NK7 A;  1V6Z A;  3AI9 X;  1UAM A;  1VHK A;  1GZ0 A;  1VHY A;  1ZJR A;  4CNF B;  3AXZ A;  3QUV A;  4IG6 A;  1UAJ A;  1V2X A;  2HA8 A;  3NK6 A;  4FAK A;  2YY8 A;  1O6D A;  3IC6 A;  1J85 A;  4CNE B;  3IEF A;  2CX8 A;  3KNU A;  4E8B A;  1TO0 A;  1UAL A;  3N4J A;  1NS5 A;  1UAK A;  1VH0 A;  3N4K A;  4CNG B; 
#chains in the KnotProt database with same CATH homology
 3ILK A;  2O3A A;  3AIA A;  3L8U A;  1P9P A;  3GYQ A;  2QWV A;  3KY7 A;  1X7O A;  3KTY A;  3ONP A;  1X7P A;  3DCM X;  3E5Y A;  1MXI A;  2QMM A;  2I6D A;  4H3Z A;  4H3Y A;  2Z0Y A;  1K3R A;  1NXZ A;  3NK7 A;  1V6Z A;  3AI9 X;  1UAM A;  1VHK A;  1GZ0 A;  1VHY A;  1ZJR A;  4CNF B;  3AXZ A;  3QUV A;  4IG6 A;  1UAJ A;  1V2X A;  2HA8 A;  3NK6 A;  4FAK A;  2YY8 A;  1O6D A;  3IC6 A;  1J85 A;  4CNE B;  3IEF A;  2CX8 A;  3KNU A;  4E8B A;  1TO0 A;  1UAL A;  3N4J A;  1NS5 A;  1UAK A;  1VH0 A;  3N4K A;  4CNG B;
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similar chains in the KnotProt database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

  
#similar chains in the KnotProt database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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How to cite
KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling