4KGNA

Crystal structure of a trna (cytidine(34)-2'-o)-methyltransferase bound to s-adenosyl homocysteine
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
139
Chain Sequence
MFNVVLVEPEIPPNTGNVIRLCANTGARLHLIEPLGFPQMRVHRDWDAFVAAEAPDPARMFAFTTRGSGRFHDRAFEPGDWFVFGAETRGLAPALVDRFAPEQRVRLPMRPGNRSLNLSNTVAVVVFEAWRQAGFEGGA
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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 a TrmH family tRNA methyltransferase bound to S-adenosyl homocysteine
rcsb
source organism Burkholderia pseudomallei
molecule tags Transferase
total genus 45
structure length 139
sequence length 156
chains with identical sequence B, C, D, E, F, G, H
other databases KnotProt 2.0: K +31
ec nomenclature ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
pdb deposition date 2013-04-29

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 4kgnA00
4YPXA 4YQOA 4YPZA 4YQ7A 4JAKA 4H3ZA 1V2XA 4CNFA 4YQ5A 3AXZA 4YPWA 4YQNA 3ONPA 4YQDA 1VH0A 5GMBA 3BBHA 2YY8A 4JALA 4MCCA 4YQAA 4YQRA 1UAMA 1J85A 3AIAA 4H3YA 1VHKA 4YVGA 1MXIA 3IEFA 2Z0YA 3KNUA 3E5YA 4YQ0A 3OINA 4YQSA 4PZKA 5GMCA 1P9PA 3ILKA 5CO4A 4YQ2A 2V3JA 5D9FA 4YQIA 3N4KA 4XBOA 3L8UA 1IPAA 4YQQA 2QMMA 2CX8A 4CNGA 4YQ9A 3O7BA 4RG1A 4E8BA 4YQKA 4YQJA 4YVHA 4X3MA 4MCBA 1X7PA 3BBDA 1Z85A 4KDZA 2EGWA 1TO0A 3IC6A 4CNDA 4YVJA 5GM8A 3OIJA 4MCDA 4YVKA 4YQ6A 1K3RA 2QWVA 4YQTA 3NK7A 4YPYA 3KTYA 3QUVA 1O6DA 3N4JA 1X7OA 4YVIA 1UAKA 1UAJA 4YQLA 2O3AA 1ZJRA 1UALA 3NK6A 4IG6A 4L69A 4YQ4A 1OY5A 1NS5A 4YQCA 1VHYA 4J3CA 3KW2A 4KGNA 2V3KA 1GZ0A 1V6ZA 3DCMX 3GYQA 3KY7A 4YQ3A 4YQ1A 4FAKA 4YQGA 4X3LA 3BBEA 4YQBA 3OIIA 3AI9X 5FAIA 1NXZA 2I6DA 4YQ8A 2EGVA 2HA8A 4CNEA 4YQPA
chains in the Genus database with same CATH superfamily
4YPXA 4YQOA 4YPZA 4YQ7A 4JAKA 4H3ZA 1V2XA 4CNFA 4YQ5A 3AXZA 4YPWA 4YQNA 3ONPA 4YQDA 1VH0A 5GMBA 3BBHA 4JWHA 2YY8A 4JALA 4MCCA 4YQAA 4YQRA 1UAMA 1J85A 3AIAA 4H3YA 4JWJA 1VHKA 4YVGA 1MXIA 3IEFA 2Z0YA 3KNUA 3E5YA 4YQ0A 3OINA 4YQSA 4PZKA 5GMCA 1P9PA 3ILKA 5CO4A 4YQ2A 2V3JA 5D9FA 4YQIA 3N4KA 4XBOA 4FMWA 3L8UA 1IPAA 4YQQA 2QMMA 2CX8A 4CNGA 4YQ9A 3O7BA 4RG1A 4E8BA 4YQKA 4YQJA 4JWFA 4YVHA 4X3MA 4MCBA 1X7PA 3BBDA 1Z85A 4KDZA 2EGWA 1TO0A 3IC6A 4CNDA 4YVJA 5GM8A 3OIJA 4MCDA 4YVKA 4YQ6A 1K3RA 2QWVA 4YQTA 3NK7A 4YPYA 3KTYA 3QUVA 1O6DA 3N4JA 1X7OA 4YVIA 1UAKA 1UAJA 4YQLA 2O3AA 1ZJRA 1UALA 3NK6A 4IG6A 4L69A 4YQ4A 1OY5A 1NS5A 4YQCA 1VHYA 4J3CA 3KW2A 4KGNA 2V3KA 1GZ0A 1V6ZA 3DCMX 3GYQA 3KY7A 4JWGA 4YQ3A 4YQ1A 4FAKA 4YQGA 4X3LA 3BBEA 4YQBA 3OIIA 3AI9X 5FAIA 1NXZA 2I6DA 4YQ8A 2EGVA 2HA8A 4CNEA 4YQPA
chains in the Genus database with same CATH topology
4YPXA 4YQOA 4YPZA 4YQ7A 4JAKA 4H3ZA 1V2XA 4CNFA 4YQ5A 3AXZA 4YPWA 4YQNA 3ONPA 4YQDA 1VH0A 5GMBA 3BBHA 4JWHA 2YY8A 4JALA 4MCCA 4YQAA 4YQRA 1UAMA 1J85A 3AIAA 4H3YA 4JWJA 1VHKA 4YVGA 1MXIA 3IEFA 2Z0YA 3KNUA 3E5YA 4YQ0A 3OINA 4YQSA 4PZKA 5GMCA 1P9PA 3ILKA 5CO4A 4YQ2A 2V3JA 5D9FA 4YQIA 3N4KA 4XBOA 4FMWA 3L8UA 1IPAA 4YQQA 2QMMA 2CX8A 4CNGA 4YQ9A 3O7BA 4RG1A 4E8BA 4YQKA 4YQJA 4JWFA 4YVHA 4X3MA 4MCBA 1X7PA 3BBDA 1Z85A 4KDZA 2EGWA 1TO0A 3IC6A 4CNDA 4YVJA 5GM8A 3OIJA 4MCDA 4YVKA 4YQ6A 1K3RA 2QWVA 4YQTA 3NK7A 4YPYA 3KTYA 3QUVA 1O6DA 3N4JA 1X7OA 4YVIA 1UAKA 1UAJA 4YQLA 2O3AA 1ZJRA 1UALA 3NK6A 4IG6A 4L69A 4YQ4A 1OY5A 1NS5A 4YQCA 1VHYA 4J3CA 3KW2A 4KGNA 2V3KA 1GZ0A 1V6ZA 3DCMX 3GYQA 3KY7A 4JWGA 4YQ3A 4YQ1A 4FAKA 4YQGA 4X3LA 3BBEA 4YQBA 3OIIA 3AI9X 5FAIA 1NXZA 2I6DA 4YQ8A 2EGVA 2HA8A 4CNEA 4YQPA
chains in the Genus database with same CATH homology


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