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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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
Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
+31 84-136 53 1-83, 137-170 83 34 knot
Chain Sequence
DPALRALQNIRIVLVETSHTGNMGSVARAMKTMGLTNLWLVNPLVKPDSQAIALAAGASDVIGNAHIVDTLDEALAGCSLVVGTSA-----PWPMLDPRECGLKSVAEAANTPVALVFGRERVGLTNEELQKCHYHVAIAANPEYSSLNLAMAVQVIAYEVRMAWLATQ
Whole chain analysis
Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1

Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
3.1 82-132 51 1-81, 133-164 81 32 knot
view details
2.1 72-129 58 1-71 135-164 130-134 71 30 slipknot
view details
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
2Z0YA 1NS5A 1J85A 3KY7A 3ONPA 2CX8A 3DCMX 1O6DA 1V6ZA 4H3ZA 1VH0A 3N4JA 4CNFB 1V2XA 1VHKA 1UAMA 1GZ0A 1UAJA 2I6DA 3IC6A 3AI9X 3NK6A 4CNGB 3L8UA 4FAKA 1P9PA 4E8BA 3ILKA 4H3YA 2HA8A 2O3AA 3NK7A 1MXIA 3IEFA 1X7OA 3AXZA 1K3RA 1VHYA 1ZJRA 2QWVA 3GYQA 1UAKA 3QUVA 4IG6A 3KNUA 1X7PA 3N4KA 1NXZA 1UALA 2QMMA 3AIAA 3E5YA 4CNEB 3KTYA 2YY8A 1TO0A
chains in the KnotProt database with same CATH superfamily
2Z0YA 1NS5A 1J85A 3KY7A 3ONPA 2CX8A 3DCMX 1O6DA 1V6ZA 4H3ZA 1VH0A 3N4JA 4CNFB 1V2XA 1VHKA 1UAMA 1GZ0A 1UAJA 2I6DA 3IC6A 3AI9X 3NK6A 4CNGB 3L8UA 4FAKA 1P9PA 4E8BA 3ILKA 4H3YA 2HA8A 2O3AA 3NK7A 1MXIA 3IEFA 1X7OA 3AXZA 1K3RA 1VHYA 1ZJRA 2QWVA 3GYQA 1UAKA 3QUVA 4IG6A 3KNUA 1X7PA 3N4KA 1NXZA 1UALA 2QMMA 3AIAA 3E5YA 4CNEB 3KTYA 2YY8A 1TO0A
chains in the KnotProt database with same CATH topology
2Z0YA 1NS5A 1J85A 3KY7A 3ONPA 2CX8A 3DCMX 1O6DA 1V6ZA 4H3ZA 1VH0A 3N4JA 4CNFB 1V2XA 1VHKA 1UAMA 1GZ0A 1UAJA 2I6DA 3IC6A 3AI9X 3NK6A 4CNGB 3L8UA 4FAKA 1P9PA 4E8BA 3ILKA 4H3YA 2HA8A 2O3AA 3NK7A 1MXIA 3IEFA 1X7OA 3AXZA 1K3RA 1VHYA 1ZJRA 2QWVA 3GYQA 1UAKA 3QUVA 4IG6A 3KNUA 1X7PA 3N4KA 1NXZA 1UALA 2QMMA 3AIAA 3E5YA 4CNEB 3KTYA 2YY8A 1TO0A
chains in the KnotProt database with same CATH homology


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