4CNGB

Crystal structure of sulfolobus acidocaldarius 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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 75-128 54 1-74, 129-156 74 28 knot
Chain Sequence
MTIRLVIVEPEGAYNLGFIARLVKNFLIDEFYVVNPKADINEAIKFSAKGSEVIEKMMKITNNFDDAIRDVDLKIATSSIAD--------SIRPIDLERLIKDKKVAFIFGRESVGLTREEIAKSDFLLFIPANPEYPVLNLSHAVGIVLYELWRN
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
view details
3.1 76-121 46 1-75, 122-148 75 27 knot
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2.1 73-118 46 1-72 124-148 119-123 72 25 slipknot
sequence length 156
structure length 148
publication title Characterization of Two Homologous 2'-O-Methyltransferases Showing Different Specificities for Their tRNA Substrates.
pubmed doi rcsb
molecule tags Transferase
molecule keywords SPOU RRNA METHYLASE
source organism Sulfolobus acidocaldarius
missing residues 83-90
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 4cngB00
1VHYA 1UAJA 4H3ZA 2QMMA 4CNEB 1X7PA 1O6DA 3KNUA 3N4KA 4E8BA 3AI9X 4FAKA 1NS5A 3IC6A 1UAMA 1TO0A 4IG6A 1J85A 2QWVA 3GYQA 1UAKA 1K3RA 1GZ0A 1VH0A 1ZJRA 1MXIA 3AIAA 3NK7A 3KY7A 3KTYA 3AXZA 1UALA 2HA8A 3ONPA 1NXZA 2I6DA 4H3YA 3ILKA 4CNFB 4CNGB 1P9PA 1V6ZA 1X7OA 2CX8A 3DCMX 3E5YA 1VHKA 2O3AA 3IEFA 3QUVA 2Z0YA 3NK6A 3N4JA 3L8UA 2YY8A 1V2XA
chains in the KnotProt database with same CATH superfamily
1VHYA 1UAJA 4H3ZA 2QMMA 4CNEB 1X7PA 1O6DA 3KNUA 3N4KA 4E8BA 3AI9X 4FAKA 1NS5A 3IC6A 1UAMA 1TO0A 4IG6A 1J85A 2QWVA 3GYQA 1UAKA 1K3RA 1GZ0A 1VH0A 1ZJRA 1MXIA 3AIAA 3NK7A 3KY7A 3KTYA 3AXZA 1UALA 2HA8A 3ONPA 1NXZA 2I6DA 4H3YA 3ILKA 4CNFB 4CNGB 1P9PA 1V6ZA 1X7OA 2CX8A 3DCMX 3E5YA 1VHKA 2O3AA 3IEFA 3QUVA 2Z0YA 3NK6A 3N4JA 3L8UA 2YY8A 1V2XA
chains in the KnotProt database with same CATH topology
1VHYA 1UAJA 4H3ZA 2QMMA 4CNEB 1X7PA 1O6DA 3KNUA 3N4KA 4E8BA 3AI9X 4FAKA 1NS5A 3IC6A 1UAMA 1TO0A 4IG6A 1J85A 2QWVA 3GYQA 1UAKA 1K3RA 1GZ0A 1VH0A 1ZJRA 1MXIA 3AIAA 3NK7A 3KY7A 3KTYA 3AXZA 1UALA 2HA8A 3ONPA 1NXZA 2I6DA 4H3YA 3ILKA 4CNFB 4CNGB 1P9PA 1V6ZA 1X7OA 2CX8A 3DCMX 3E5YA 1VHKA 2O3AA 3IEFA 3QUVA 2Z0YA 3NK6A 3N4JA 3L8UA 2YY8A 1V2XA
chains in the KnotProt database with same CATH homology

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