4KDZA

Crystal structure of trna/rrna methyltransferase yibk from escherichia coli (target nysgrc-012599)
Total Genus 46
Loading diagram...

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
b'MLNIVLYEPEIPPNTGNIIRLCANTGFRLHIIEPMGFAWDDKRLRRAGLDYHEFTAVTRHHDYRAFLEAENPQRLFALTTKGTPAHSAVSYQDGDYLMFGPETRGLPASILDALPAEQKIRIPMVPDSRSMNLSNAVSVVVYEAWRQLGYPGAVLR'
Loading diagram...

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


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...