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


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