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


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