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


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