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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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

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