1J85A

Structure of yibk from haemophilus influenzae (hi0766), a truncated sequence homolog of trna (guanosine-2'-o-) methyltransferase (spou)
Total Genus 44
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
44
Knots found
sequence length
156
structure length
156
Chain Sequence
MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGAVNL
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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molecule tags Transferase
molecule keywords YibK
publication title Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): A cofactor bound at a site formed by a knot
pubmed doi rcsb
source organism Haemophilus influenzae rd
total genus 44
structure length 156
sequence length 156
other databases KnotProt 2.0: K +31
ec nomenclature ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
pdb deposition date 2001-05-20

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
4X3MA 4YQLA 4CNEA 4YQ1A 4RG1A 5GMBA 3N4KA 2EGWA 3O7BA 4YVIA 4YPWA 4YPYA 1K3RA 1J85A 4KGNA 4JAKA 1OY5A 1X7PA 4YVJA 3OINA 3AXZA 1UAKA 4YQQA 4MCCA 4YPXA 4IG6A 1ZJRA 5GMCA 4YQJA 1X7OA 4MCBA 2V3JA 4YQSA 3BBHA 4YQAA 4YVKA 4FAKA 1V6ZA 4CNGA 3GYQA 1IPAA 3NK7A 3BBEA 2EGVA 4YQ0A 2V3KA 2QMMA 4YQ6A 4H3YA 1V2XA 5FAIA 3KTYA 3N4JA 4CNFA 3QUVA 3DCMX 4YQGA 4X3LA 1VH0A 3ILKA 3AIAA 2QWVA 4YQBA 4J3CA 4YQ9A 4YQ5A 1NXZA 2Z0YA 1NS5A 2I6DA 2YY8A 5GM8A 3KNUA 4YQPA 5CO4A 1UALA 4YQDA 4E8BA 4YQOA 3OIJA 4YPZA 4YVHA 4H3ZA 4YQTA 3OIIA 1Z85A 3E5YA 4MCDA 1O6DA 4YVGA 4YQ2A 4YQRA 1P9PA 2O3AA 4YQ4A 2CX8A 1GZ0A 1UAMA 3IEFA 3BBDA 3ONPA 4YQKA 3L8UA 4YQCA 4YQNA 1VHKA 4YQIA 1VHYA 4KDZA 4YQ7A 3KW2A 4JALA 3IC6A 2HA8A 1MXIA 4XBOA 3AI9X 1TO0A 4PZKA 4CNDA 1UAJA 4L69A 5D9FA 4YQ3A 4YQ8A 3KY7A 3NK6A
chains in the Genus database with same CATH superfamily
4X3MA 4YQLA 4CNEA 4YQ1A 4RG1A 5GMBA 3N4KA 4JWFA 2EGWA 3O7BA 4YVIA 4YPWA 4YPYA 1K3RA 4JWHA 4FMWA 1J85A 4KGNA 4JAKA 1OY5A 1X7PA 4YVJA 3OINA 3AXZA 1UAKA 4YQQA 4MCCA 4YPXA 4IG6A 1ZJRA 5GMCA 4YQJA 1X7OA 4MCBA 2V3JA 4YQSA 3BBHA 4YQAA 4YVKA 4FAKA 1V6ZA 4CNGA 3GYQA 1IPAA 3NK7A 3BBEA 2EGVA 4YQ0A 2V3KA 2QMMA 4YQ6A 4H3YA 1V2XA 5FAIA 3KTYA 3N4JA 4CNFA 3QUVA 4JWJA 3DCMX 4YQGA 4X3LA 1VH0A 3ILKA 3AIAA 2QWVA 4YQBA 4J3CA 4JWGA 4YQ9A 4YQ5A 1NXZA 2Z0YA 1NS5A 2I6DA 2YY8A 5GM8A 3KNUA 4YQPA 5CO4A 1UALA 4YQDA 4E8BA 4YQOA 3OIJA 4YPZA 4YVHA 4H3ZA 4YQTA 3OIIA 1Z85A 3E5YA 4MCDA 1O6DA 4YVGA 4YQ2A 4YQRA 1P9PA 2O3AA 4YQ4A 2CX8A 1GZ0A 1UAMA 3IEFA 3BBDA 3ONPA 4YQKA 3L8UA 4YQCA 4YQNA 1VHKA 4YQIA 1VHYA 4KDZA 4YQ7A 3KW2A 4JALA 3IC6A 2HA8A 1MXIA 4XBOA 3AI9X 1TO0A 4PZKA 4CNDA 1UAJA 4L69A 5D9FA 4YQ3A 4YQ8A 3KY7A 3NK6A
chains in the Genus database with same CATH topology
4X3MA 4YQLA 4CNEA 4YQ1A 4RG1A 5GMBA 3N4KA 4JWFA 2EGWA 3O7BA 4YVIA 4YPWA 4YPYA 1K3RA 4JWHA 4FMWA 1J85A 4KGNA 4JAKA 1OY5A 1X7PA 4YVJA 3OINA 3AXZA 1UAKA 4YQQA 4MCCA 4YPXA 4IG6A 1ZJRA 5GMCA 4YQJA 1X7OA 4MCBA 2V3JA 4YQSA 3BBHA 4YQAA 4YVKA 4FAKA 1V6ZA 4CNGA 3GYQA 1IPAA 3NK7A 3BBEA 2EGVA 4YQ0A 2V3KA 2QMMA 4YQ6A 4H3YA 1V2XA 5FAIA 3KTYA 3N4JA 4CNFA 3QUVA 4JWJA 3DCMX 4YQGA 4X3LA 1VH0A 3ILKA 3AIAA 2QWVA 4YQBA 4J3CA 4JWGA 4YQ9A 4YQ5A 1NXZA 2Z0YA 1NS5A 2I6DA 2YY8A 5GM8A 3KNUA 4YQPA 5CO4A 1UALA 4YQDA 4E8BA 4YQOA 3OIJA 4YPZA 4YVHA 4H3ZA 4YQTA 3OIIA 1Z85A 3E5YA 4MCDA 1O6DA 4YVGA 4YQ2A 4YQRA 1P9PA 2O3AA 4YQ4A 2CX8A 1GZ0A 1UAMA 3IEFA 3BBDA 3ONPA 4YQKA 3L8UA 4YQCA 4YQNA 1VHKA 4YQIA 1VHYA 4KDZA 4YQ7A 3KW2A 4JALA 3IC6A 2HA8A 1MXIA 4XBOA 3AI9X 1TO0A 4PZKA 4CNDA 1UAJA 4L69A 5D9FA 4YQ3A 4YQ8A 3KY7A 3NK6A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4X3M A;  4YQL A;  4CNE A;  4YQ1 A;  4RG1 A;  5GMB A;  3N4K A;  2EGW A;  3O7B A;  4YVI A;  4YPW A;  4YPY A;  1K3R A;  1J85 A;  4KGN A;  4JAK A;  1OY5 A;  1X7P A;  4YVJ A;  3OIN A;  3AXZ A;  1UAK A;  4YQQ A;  4MCC A;  4YPX A;  4IG6 A;  1ZJR A;  5GMC A;  4YQJ A;  1X7O A;  4MCB A;  2V3J A;  4YQS A;  3BBH A;  4YQA A;  4YVK A;  4FAK A;  1V6Z A;  4CNG A;  3GYQ A;  1IPA A;  3NK7 A;  3BBE A;  2EGV A;  4YQ0 A;  2V3K A;  2QMM A;  4YQ6 A;  4H3Y A;  1V2X A;  5FAI A;  3KTY A;  3N4J A;  4CNF A;  3QUV A;  3DCM X;  4YQG A;  4X3L A;  1VH0 A;  3ILK A;  3AIA A;  2QWV A;  4YQB A;  4J3C A;  4YQ9 A;  4YQ5 A;  1NXZ A;  2Z0Y A;  1NS5 A;  2I6D A;  2YY8 A;  5GM8 A;  3KNU A;  4YQP A;  5CO4 A;  1UAL A;  4YQD A;  4E8B A;  4YQO A;  3OIJ A;  4YPZ A;  4YVH A;  4H3Z A;  4YQT A;  3OII A;  1Z85 A;  3E5Y A;  4MCD A;  1O6D A;  4YVG A;  4YQ2 A;  4YQR A;  1P9P A;  2O3A A;  4YQ4 A;  2CX8 A;  1GZ0 A;  1UAM A;  3IEF A;  3BBD A;  3ONP A;  4YQK A;  3L8U A;  4YQC A;  4YQN A;  1VHK A;  4YQI A;  1VHY A;  4KDZ A;  4YQ7 A;  3KW2 A;  4JAL A;  3IC6 A;  2HA8 A;  1MXI A;  4XBO A;  3AI9 X;  1TO0 A;  4PZK A;  4CND A;  1UAJ A;  4L69 A;  5D9F A;  4YQ3 A;  4YQ8 A;  3KY7 A;  3NK6 A; 
#chains in the Genus database with same CATH topology
 4X3M A;  4YQL A;  4CNE A;  4YQ1 A;  4RG1 A;  5GMB A;  3N4K A;  4JWF A;  2EGW A;  3O7B A;  4YVI A;  4YPW A;  4YPY A;  1K3R A;  4JWH A;  4FMW A;  1J85 A;  4KGN A;  4JAK A;  1OY5 A;  1X7P A;  4YVJ A;  3OIN A;  3AXZ A;  1UAK A;  4YQQ A;  4MCC A;  4YPX A;  4IG6 A;  1ZJR A;  5GMC A;  4YQJ A;  1X7O A;  4MCB A;  2V3J A;  4YQS A;  3BBH A;  4YQA A;  4YVK A;  4FAK A;  1V6Z A;  4CNG A;  3GYQ A;  1IPA A;  3NK7 A;  3BBE A;  2EGV A;  4YQ0 A;  2V3K A;  2QMM A;  4YQ6 A;  4H3Y A;  1V2X A;  5FAI A;  3KTY A;  3N4J A;  4CNF A;  3QUV A;  4JWJ A;  3DCM X;  4YQG A;  4X3L A;  1VH0 A;  3ILK A;  3AIA A;  2QWV A;  4YQB A;  4J3C A;  4JWG A;  4YQ9 A;  4YQ5 A;  1NXZ A;  2Z0Y A;  1NS5 A;  2I6D A;  2YY8 A;  5GM8 A;  3KNU A;  4YQP A;  5CO4 A;  1UAL A;  4YQD A;  4E8B A;  4YQO A;  3OIJ A;  4YPZ A;  4YVH A;  4H3Z A;  4YQT A;  3OII A;  1Z85 A;  3E5Y A;  4MCD A;  1O6D A;  4YVG A;  4YQ2 A;  4YQR A;  1P9P A;  2O3A A;  4YQ4 A;  2CX8 A;  1GZ0 A;  1UAM A;  3IEF A;  3BBD A;  3ONP A;  4YQK A;  3L8U A;  4YQC A;  4YQN A;  1VHK A;  4YQI A;  1VHY A;  4KDZ A;  4YQ7 A;  3KW2 A;  4JAL A;  3IC6 A;  2HA8 A;  1MXI A;  4XBO A;  3AI9 X;  1TO0 A;  4PZK A;  4CND A;  1UAJ A;  4L69 A;  5D9F A;  4YQ3 A;  4YQ8 A;  3KY7 A;  3NK6 A; 
#chains in the Genus database with same CATH homology
 4X3M A;  4YQL A;  4CNE A;  4YQ1 A;  4RG1 A;  5GMB A;  3N4K A;  4JWF A;  2EGW A;  3O7B A;  4YVI A;  4YPW A;  4YPY A;  1K3R A;  4JWH A;  4FMW A;  1J85 A;  4KGN A;  4JAK A;  1OY5 A;  1X7P A;  4YVJ A;  3OIN A;  3AXZ A;  1UAK A;  4YQQ A;  4MCC A;  4YPX A;  4IG6 A;  1ZJR A;  5GMC A;  4YQJ A;  1X7O A;  4MCB A;  2V3J A;  4YQS A;  3BBH A;  4YQA A;  4YVK A;  4FAK A;  1V6Z A;  4CNG A;  3GYQ A;  1IPA A;  3NK7 A;  3BBE A;  2EGV A;  4YQ0 A;  2V3K A;  2QMM A;  4YQ6 A;  4H3Y A;  1V2X A;  5FAI A;  3KTY A;  3N4J A;  4CNF A;  3QUV A;  4JWJ A;  3DCM X;  4YQG A;  4X3L A;  1VH0 A;  3ILK A;  3AIA A;  2QWV A;  4YQB A;  4J3C A;  4JWG A;  4YQ9 A;  4YQ5 A;  1NXZ A;  2Z0Y A;  1NS5 A;  2I6D A;  2YY8 A;  5GM8 A;  3KNU A;  4YQP A;  5CO4 A;  1UAL A;  4YQD A;  4E8B A;  4YQO A;  3OIJ A;  4YPZ A;  4YVH A;  4H3Z A;  4YQT A;  3OII A;  1Z85 A;  3E5Y A;  4MCD A;  1O6D A;  4YVG A;  4YQ2 A;  4YQR A;  1P9P A;  2O3A A;  4YQ4 A;  2CX8 A;  1GZ0 A;  1UAM A;  3IEF A;  3BBD A;  3ONP A;  4YQK A;  3L8U A;  4YQC A;  4YQN A;  1VHK A;  4YQI A;  1VHY A;  4KDZ A;  4YQ7 A;  3KW2 A;  4JAL A;  3IC6 A;  2HA8 A;  1MXI A;  4XBO A;  3AI9 X;  1TO0 A;  4PZK A;  4CND A;  1UAJ A;  4L69 A;  5D9F A;  4YQ3 A;  4YQ8 A;  3KY7 A;  3NK6 A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus 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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