4KDZA

Crystal structure of trna/rrna methyltransferase yibk from escherichia coli (target nysgrc-012599)
Total Genus 46
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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
46
Knots found
sequence length
156
structure length
156
Chain Sequence
MLNIVLYEPEIPPNTGNIIRLCANTGFRLHIIEPMGFAWDDKRLRRAGLDYHEFTAVTRHHDYRAFLEAENPQRLFALTTKGTPAHSAVSYQDGDYLMFGPETRGLPASILDALPAEQKIRIPMVPDSRSMNLSNAVSVVVYEAWRQLGYPGAVLR
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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 tRNA (cytidine(34)-2'-O)-methyltransferase
publication title Crystal structure of tRNA/rRNA methyltransferase YibK from Escherichia coli (Target NYSGRC-012599)
rcsb
source organism Escherichia coli
molecule tags Transferase
total genus 46
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 2013-04-25

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 4kdzA00
4YPXA 4CNGA 3OINA 2I6DA 4YQCA 4YQJA 3ONPA 4YVHA 1UALA 3KNUA 4MCBA 3DCMX 4YQRA 4IG6A 2QWVA 4CNFA 5CO4A 3OIIA 1NXZA 4YVIA 1UAJA 4YQ4A 3BBDA 1V6ZA 4YQAA 4YQLA 4YVKA 3E5YA 1GZ0A 4YPWA 3KTYA 4YPYA 5GMBA 3AIAA 1VH0A 4YQPA 4CNEA 2YY8A 4MCCA 5GMCA 4X3MA 1UAMA 1V2XA 4YQKA 1UAKA 3BBEA 1OY5A 5GM8A 5FAIA 4CNDA 1K3RA 3N4JA 4YQIA 4YQTA 3GYQA 1NS5A 4H3ZA 2O3AA 1P9PA 1X7PA 4YVJA 4YQBA 3NK6A 3BBHA 3IEFA 3OIJA 2Z0YA 4YQ7A 4YQQA 4KDZA 3L8UA 4YQ8A 4YQDA 1X7OA 4YQGA 1VHYA 3AXZA 3KW2A 4YQSA 4YQ2A 3NK7A 4KGNA 1MXIA 2EGVA 4YQ9A 4X3LA 4YQ1A 2QMMA 2EGWA 4PZKA 3N4KA 2HA8A 4YVGA 4YQ6A 4YQNA 3QUVA 2V3JA 4FAKA 1ZJRA 1TO0A 3O7BA 4YPZA 4J3CA 4YQ5A 4JALA 4MCDA 4YQ0A 2CX8A 1J85A 4XBOA 3IC6A 4YQOA 4E8BA 2V3KA 4JAKA 4H3YA 1IPAA 3AI9X 1O6DA 4RG1A 4YQ3A 4L69A 1VHKA 5D9FA 3ILKA 3KY7A 1Z85A
chains in the Genus database with same CATH superfamily
4YPXA 4CNGA 3OINA 2I6DA 4YQCA 4YQJA 3ONPA 4YVHA 1UALA 3KNUA 4MCBA 4JWGA 3DCMX 4YQRA 4IG6A 2QWVA 4CNFA 5CO4A 3OIIA 1NXZA 4YVIA 1UAJA 4YQ4A 3BBDA 1V6ZA 4YQAA 4YQLA 4JWJA 4YVKA 3E5YA 1GZ0A 4YPWA 3KTYA 4YPYA 5GMBA 3AIAA 1VH0A 4YQPA 4CNEA 2YY8A 4MCCA 5GMCA 4X3MA 1UAMA 1V2XA 4YQKA 1UAKA 3BBEA 1OY5A 5GM8A 5FAIA 4CNDA 1K3RA 3N4JA 4YQIA 4YQTA 3GYQA 1NS5A 4H3ZA 2O3AA 1P9PA 1X7PA 4YVJA 4YQBA 3NK6A 3BBHA 3IEFA 3OIJA 2Z0YA 4YQ7A 4YQQA 4KDZA 3L8UA 4YQ8A 4YQDA 1X7OA 4YQGA 1VHYA 3AXZA 3KW2A 4YQSA 4YQ2A 3NK7A 4KGNA 1MXIA 2EGVA 4YQ9A 4X3LA 4YQ1A 2QMMA 2EGWA 4PZKA 3N4KA 2HA8A 4YVGA 4YQ6A 4YQNA 3QUVA 2V3JA 4FAKA 4JWHA 1ZJRA 1TO0A 3O7BA 4YPZA 4J3CA 4YQ5A 4JALA 4MCDA 4YQ0A 2CX8A 4JWFA 1J85A 4XBOA 3IC6A 4YQOA 4E8BA 2V3KA 4JAKA 4H3YA 1IPAA 3AI9X 1O6DA 4RG1A 4FMWA 4YQ3A 4L69A 1VHKA 5D9FA 3ILKA 3KY7A 1Z85A
chains in the Genus database with same CATH topology
4YPXA 4CNGA 3OINA 2I6DA 4YQCA 4YQJA 3ONPA 4YVHA 1UALA 3KNUA 4MCBA 4JWGA 3DCMX 4YQRA 4IG6A 2QWVA 4CNFA 5CO4A 3OIIA 1NXZA 4YVIA 1UAJA 4YQ4A 3BBDA 1V6ZA 4YQAA 4YQLA 4JWJA 4YVKA 3E5YA 1GZ0A 4YPWA 3KTYA 4YPYA 5GMBA 3AIAA 1VH0A 4YQPA 4CNEA 2YY8A 4MCCA 5GMCA 4X3MA 1UAMA 1V2XA 4YQKA 1UAKA 3BBEA 1OY5A 5GM8A 5FAIA 4CNDA 1K3RA 3N4JA 4YQIA 4YQTA 3GYQA 1NS5A 4H3ZA 2O3AA 1P9PA 1X7PA 4YVJA 4YQBA 3NK6A 3BBHA 3IEFA 3OIJA 2Z0YA 4YQ7A 4YQQA 4KDZA 3L8UA 4YQ8A 4YQDA 1X7OA 4YQGA 1VHYA 3AXZA 3KW2A 4YQSA 4YQ2A 3NK7A 4KGNA 1MXIA 2EGVA 4YQ9A 4X3LA 4YQ1A 2QMMA 2EGWA 4PZKA 3N4KA 2HA8A 4YVGA 4YQ6A 4YQNA 3QUVA 2V3JA 4FAKA 4JWHA 1ZJRA 1TO0A 3O7BA 4YPZA 4J3CA 4YQ5A 4JALA 4MCDA 4YQ0A 2CX8A 4JWFA 1J85A 4XBOA 3IC6A 4YQOA 4E8BA 2V3KA 4JAKA 4H3YA 1IPAA 3AI9X 1O6DA 4RG1A 4FMWA 4YQ3A 4L69A 1VHKA 5D9FA 3ILKA 3KY7A 1Z85A
chains in the Genus database with same CATH homology


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