1J85A

Structure of yibk from haemophilus influenzae (hi0766), a truncated sequence homolog of trna (guanosine-2'-o-) methyltransferase (spou)
Warning
  • Chain breaks within knotoid 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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Genus: 44
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 78-119 42 1-77, 120-155 77 36 knot
Chain Sequence
MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGAVNL
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 76-137 62 1-75, 138-156 75 19 knot
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3.1 76-120 45 1-75 138-156 121-137 75 19 slipknot
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2.1 80-122 43 123-156 1-75 76-79 75 33 slipknot
sequence length 156
structure length 156
publication title Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): A cofactor bound at a site formed by a knot
pubmed doi rcsb
molecule tags Transferase
molecule keywords YibK
source organism Haemophilus influenzae rd
total genus Genus: 44
ec nomenclature ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
pdb deposition date 2001-05-20
KnotProt deposition date 2018-08-14

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A 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 1j85A00
2QMMA 3IC6A 3N4KA 2YY8A 1X7PA 4H3ZA 1ZJRA 4CNEB 3AI9X 1P9PA 3NK6A 1UAKA 1UAMA 3NK7A 1GZ0A 2O3AA 1NXZA 4CNFB 1VHKA 1V6ZA 1VH0A 1O6DA 3N4JA 4CNGB 3IEFA 2I6DA 3ILKA 2QWVA 3KY7A 2HA8A 1V2XA 3KTYA 3GYQA 4IG6A 4H3YA 3ONPA 1TO0A 1UAJA 1VHYA 1J85A 1MXIA 4FAKA 1K3RA 3E5YA 3AXZA 1X7OA 3AIAA 3DCMX 1UALA 3L8UA 3KNUA 4E8BA 2CX8A 2Z0YA 3QUVA 1NS5A
chains in the KnotProt database with same CATH superfamily
2QMMA 3IC6A 3N4KA 2YY8A 1X7PA 4H3ZA 1ZJRA 4CNEB 3AI9X 1P9PA 3NK6A 1UAKA 1UAMA 3NK7A 1GZ0A 2O3AA 1NXZA 4CNFB 1VHKA 1V6ZA 1VH0A 1O6DA 3N4JA 4CNGB 3IEFA 2I6DA 3ILKA 2QWVA 3KY7A 2HA8A 1V2XA 3KTYA 3GYQA 4IG6A 4H3YA 3ONPA 1TO0A 1UAJA 1VHYA 1J85A 1MXIA 4FAKA 1K3RA 3E5YA 3AXZA 1X7OA 3AIAA 3DCMX 1UALA 3L8UA 3KNUA 4E8BA 2CX8A 2Z0YA 3QUVA 1NS5A
chains in the KnotProt database with same CATH topology
2QMMA 3IC6A 3N4KA 2YY8A 1X7PA 4H3ZA 1ZJRA 4CNEB 3AI9X 1P9PA 3NK6A 1UAKA 1UAMA 3NK7A 1GZ0A 2O3AA 1NXZA 4CNFB 1VHKA 1V6ZA 1VH0A 1O6DA 3N4JA 4CNGB 3IEFA 2I6DA 3ILKA 2QWVA 3KY7A 2HA8A 1V2XA 3KTYA 3GYQA 4IG6A 4H3YA 3ONPA 1TO0A 1UAJA 1VHYA 1J85A 1MXIA 4FAKA 1K3RA 3E5YA 3AXZA 1X7OA 3AIAA 3DCMX 1UALA 3L8UA 3KNUA 4E8BA 2CX8A 2Z0YA 3QUVA 1NS5A
chains in the KnotProt database with same CATH homology

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