1MXIA

Structure of yibk from haemophilus influenzae (hi0766): a methyltransferase with a cofactor bound at a site formed by a knot
Total Genus 45
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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
45
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 Hypothetical tRNA/rRNA methyltransferase HI0766
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
molecule tags Transferase
total genus 45
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 2002-10-02

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 1mxiA00
4MCDA 5FAIA 4FAKA 4YQKA 3NK7A 4CNDA 3ONPA 3AXZA 1UAKA 4MCBA 5D9FA 3KTYA 4YQSA 1V2XA 3N4JA 2V3JA 4YVHA 5GMBA 3OIJA 4XBOA 4YQ3A 1K3RA 4MCCA 4YQ7A 3E5YA 4X3LA 3DCMX 3NK6A 1NS5A 3GYQA 4YQIA 3IC6A 4YQPA 4PZKA 4IG6A 2YY8A 4JALA 1MXIA 1UALA 4H3ZA 4YQGA 5GMCA 3KW2A 1V6ZA 2V3KA 1X7PA 3IEFA 4X3MA 2QWVA 3BBEA 1Z85A 1J85A 2HA8A 4YQQA 4YQJA 1O6DA 4YQAA 3BBHA 3N4KA 3OINA 1TO0A 4CNGA 4YQRA 4YPXA 4YQTA 1P9PA 1VHKA 4YPZA 4KDZA 3O7BA 4YPWA 2QMMA 1NXZA 3OIIA 3QUVA 3KNUA 4YVKA 4JAKA 4YQ5A 2O3AA 4YQ4A 2EGVA 4YVJA 1X7OA 2Z0YA 3AI9X 2EGWA 4KGNA 3L8UA 1VH0A 4CNFA 5CO4A 4YQ0A 1VHYA 4H3YA 3KY7A 3ILKA 4L69A 4E8BA 4YQ2A 4YQOA 4YQNA 1UAJA 4RG1A 1OY5A 3AIAA 4YQDA 4YVIA 5GM8A 1IPAA 4YVGA 1UAMA 2CX8A 4CNEA 4YQ1A 3BBDA 4YQ8A 4YQ9A 4YQ6A 1ZJRA 1GZ0A 4YQCA 4YPYA 4YQLA 2I6DA 4J3CA 4YQBA
chains in the Genus database with same CATH superfamily
4MCDA 5FAIA 4FAKA 4YQKA 3NK7A 4CNDA 3ONPA 3AXZA 1UAKA 4MCBA 5D9FA 4JWJA 3KTYA 4YQSA 1V2XA 3N4JA 2V3JA 4YVHA 5GMBA 3OIJA 4XBOA 4YQ3A 1K3RA 4MCCA 4YQ7A 3E5YA 4X3LA 3DCMX 3NK6A 1NS5A 3GYQA 4JWGA 4YQIA 3IC6A 4YQPA 4PZKA 4IG6A 2YY8A 4JALA 1MXIA 1UALA 4H3ZA 4YQGA 5GMCA 3KW2A 1V6ZA 2V3KA 1X7PA 3IEFA 4X3MA 2QWVA 3BBEA 1Z85A 1J85A 2HA8A 4YQQA 4YQJA 1O6DA 4YQAA 3BBHA 3N4KA 3OINA 4JWHA 1TO0A 4CNGA 4YQRA 4YPXA 4YQTA 1P9PA 1VHKA 4YPZA 4KDZA 3O7BA 4YPWA 2QMMA 1NXZA 3OIIA 3QUVA 3KNUA 4FMWA 4YVKA 4JAKA 4YQ5A 2O3AA 4YQ4A 2EGVA 4YVJA 1X7OA 2Z0YA 3AI9X 2EGWA 4KGNA 3L8UA 1VH0A 4CNFA 5CO4A 4YQ0A 1VHYA 4H3YA 3KY7A 3ILKA 4L69A 4E8BA 4YQ2A 4YQOA 4YQNA 1UAJA 4RG1A 1OY5A 3AIAA 4YQDA 4YVIA 5GM8A 1IPAA 4YVGA 1UAMA 2CX8A 4JWFA 4CNEA 4YQ1A 3BBDA 4YQ8A 4YQ9A 4YQ6A 1ZJRA 1GZ0A 4YQCA 4YPYA 4YQLA 2I6DA 4J3CA 4YQBA
chains in the Genus database with same CATH topology
4MCDA 5FAIA 4FAKA 4YQKA 3NK7A 4CNDA 3ONPA 3AXZA 1UAKA 4MCBA 5D9FA 4JWJA 3KTYA 4YQSA 1V2XA 3N4JA 2V3JA 4YVHA 5GMBA 3OIJA 4XBOA 4YQ3A 1K3RA 4MCCA 4YQ7A 3E5YA 4X3LA 3DCMX 3NK6A 1NS5A 3GYQA 4JWGA 4YQIA 3IC6A 4YQPA 4PZKA 4IG6A 2YY8A 4JALA 1MXIA 1UALA 4H3ZA 4YQGA 5GMCA 3KW2A 1V6ZA 2V3KA 1X7PA 3IEFA 4X3MA 2QWVA 3BBEA 1Z85A 1J85A 2HA8A 4YQQA 4YQJA 1O6DA 4YQAA 3BBHA 3N4KA 3OINA 4JWHA 1TO0A 4CNGA 4YQRA 4YPXA 4YQTA 1P9PA 1VHKA 4YPZA 4KDZA 3O7BA 4YPWA 2QMMA 1NXZA 3OIIA 3QUVA 3KNUA 4FMWA 4YVKA 4JAKA 4YQ5A 2O3AA 4YQ4A 2EGVA 4YVJA 1X7OA 2Z0YA 3AI9X 2EGWA 4KGNA 3L8UA 1VH0A 4CNFA 5CO4A 4YQ0A 1VHYA 4H3YA 3KY7A 3ILKA 4L69A 4E8BA 4YQ2A 4YQOA 4YQNA 1UAJA 4RG1A 1OY5A 3AIAA 4YQDA 4YVIA 5GM8A 1IPAA 4YVGA 1UAMA 2CX8A 4JWFA 4CNEA 4YQ1A 3BBDA 4YQ8A 4YQ9A 4YQ6A 1ZJRA 1GZ0A 4YQCA 4YPYA 4YQLA 2I6DA 4J3CA 4YQBA
chains in the Genus database with same CATH homology


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