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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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

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