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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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

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