1J85A

Structure of yibk from haemophilus influenzae (hi0766), a truncated sequence homolog of trna (guanosine-2'-o-) methyltransferase (spou)
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
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+31 78-119 42 1-77, 120-155 77 36 knot
Chain Sequence
MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGAVNL
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 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
view details
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.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
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
1V6ZA 2CX8A 4H3YA 1VHKA 2QWVA 2QMMA 1VH0A 1UALA 1UAMA 4E8BA 1V2XA 1J85A 3GYQA 4CNEB 1P9PA 1VHYA 3ONPA 3NK7A 1UAKA 3NK6A 1NXZA 1UAJA 4FAKA 3KTYA 3L8UA 4CNFB 4CNGB 3N4JA 1MXIA 2I6DA 3AI9X 4IG6A 1GZ0A 1X7OA 3AXZA 3IEFA 2Z0YA 3QUVA 3DCMX 1IPAA 2O3AA 2HA8A 3N4KA 1ZJRA 3KY7A 3E5YA 1NS5A 1TO0A 3AIAA 1O6DA 3IC6A 3ILKA 3KNUA 1K3RA 2YY8A 1X7PA 4H3ZA
chains in the KnotProt database with same CATH superfamily
1V6ZA 2CX8A 4H3YA 1VHKA 2QWVA 2QMMA 1VH0A 1UALA 1UAMA 4E8BA 1V2XA 1J85A 3GYQA 4CNEB 1P9PA 1VHYA 3ONPA 3NK7A 1UAKA 3NK6A 1NXZA 1UAJA 4FAKA 3KTYA 3L8UA 4CNFB 4CNGB 3N4JA 1MXIA 2I6DA 3AI9X 4IG6A 1GZ0A 1X7OA 3AXZA 3IEFA 2Z0YA 3QUVA 3DCMX 1IPAA 2O3AA 2HA8A 3N4KA 1ZJRA 3KY7A 3E5YA 1NS5A 1TO0A 3AIAA 1O6DA 3IC6A 3ILKA 3KNUA 1K3RA 2YY8A 1X7PA 4H3ZA
chains in the KnotProt database with same CATH topology
1V6ZA 2CX8A 4H3YA 1VHKA 2QWVA 2QMMA 1VH0A 1UALA 1UAMA 4E8BA 1V2XA 1J85A 3GYQA 4CNEB 1P9PA 1VHYA 3ONPA 3NK7A 1UAKA 3NK6A 1NXZA 1UAJA 4FAKA 3KTYA 3L8UA 4CNFB 4CNGB 3N4JA 1MXIA 2I6DA 3AI9X 4IG6A 1GZ0A 1X7OA 3AXZA 3IEFA 2Z0YA 3QUVA 3DCMX 1IPAA 2O3AA 2HA8A 3N4KA 1ZJRA 3KY7A 3E5YA 1NS5A 1TO0A 3AIAA 1O6DA 3IC6A 3ILKA 3KNUA 1K3RA 2YY8A 1X7PA 4H3ZA
chains in the KnotProt database with same CATH homology


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