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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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
4CNFB 2QMMA 3E5YA 2O3AA 3ILKA 2YY8A 1K3RA 3ONPA 1O6DA 1UAMA 4IG6A 3KY7A 3NK6A 1ZJRA 1X7PA 1NS5A 1VHYA 2HA8A 1VHKA 4H3ZA 1VH0A 3GYQA 3N4KA 3QUVA 3DCMX 3KNUA 3N4JA 3NK7A 1J85A 1NXZA 1MXIA 1X7OA 3IC6A 1TO0A 1V2XA 1P9PA 4FAKA 1UAKA 1V6ZA 3AI9X 1UALA 2I6DA 4CNGB 1GZ0A 3KTYA 2Z0YA 3IEFA 3L8UA 4H3YA 4CNEB 3AXZA 2QWVA 4E8BA 1UAJA 2CX8A 3AIAA
chains in the KnotProt database with same CATH superfamily
4CNFB 2QMMA 3E5YA 2O3AA 3ILKA 2YY8A 1K3RA 3ONPA 1O6DA 1UAMA 4IG6A 3KY7A 3NK6A 1ZJRA 1X7PA 1NS5A 1VHYA 2HA8A 1VHKA 4H3ZA 1VH0A 3GYQA 3N4KA 3QUVA 3DCMX 3KNUA 3N4JA 3NK7A 1J85A 1NXZA 1MXIA 1X7OA 3IC6A 1TO0A 1V2XA 1P9PA 4FAKA 1UAKA 1V6ZA 3AI9X 1UALA 2I6DA 4CNGB 1GZ0A 3KTYA 2Z0YA 3IEFA 3L8UA 4H3YA 4CNEB 3AXZA 2QWVA 4E8BA 1UAJA 2CX8A 3AIAA
chains in the KnotProt database with same CATH topology
4CNFB 2QMMA 3E5YA 2O3AA 3ILKA 2YY8A 1K3RA 3ONPA 1O6DA 1UAMA 4IG6A 3KY7A 3NK6A 1ZJRA 1X7PA 1NS5A 1VHYA 2HA8A 1VHKA 4H3ZA 1VH0A 3GYQA 3N4KA 3QUVA 3DCMX 3KNUA 3N4JA 3NK7A 1J85A 1NXZA 1MXIA 1X7OA 3IC6A 1TO0A 1V2XA 1P9PA 4FAKA 1UAKA 1V6ZA 3AI9X 1UALA 2I6DA 4CNGB 1GZ0A 3KTYA 2Z0YA 3IEFA 3L8UA 4H3YA 4CNEB 3AXZA 2QWVA 4E8BA 1UAJA 2CX8A 3AIAA
chains in the KnotProt database with same CATH homology

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