2YY8A

Crystal structure of archaeal trna-methylase for position 56 (atrm56) from pyrococcus horikoshii, complexed with s-adenosyl-l-methionine
Total Genus 54
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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
54
Knots found
sequence length
175
structure length
174
Chain Sequence
MIVVLRLGHRPEDKRVTTHVALTARAFGADGIIIASEEDEKVKESVEDVVKRWGGPFFIEFNRNWRKVMKEFTGVKVHLTMYGLHVDDVIEELKEKLKKGEDFMIIVGAEKVPREVYELADYNVAIGNQPHSEVAALAVLLDRLLEGKGLKKEFKGAKIKIVPQARGKKVVEVQ
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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 UPF0106 protein PH0461
publication title Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA
pubmed doi rcsb
source organism Pyrococcus horikoshii
molecule tags Transferase
total genus 54
structure length 174
sequence length 175
chains with identical sequence B
other databases KnotProt 2.0: K +31
ec nomenclature ec 2.1.1.206: tRNA (cytidine(56)-2'-O)-methyltransferase.
pdb deposition date 2007-04-27

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01994 Trm56 tRNA ribose 2'-O-methyltransferase, aTrm56
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 2yy8A00
2QWVA 4H3ZA 4YVGA 4YQQA 4YPZA 4YPWA 4E8BA 1GZ0A 4YQ8A 3QUVA 4KDZA 4X3LA 3BBDA 4XBOA 1VHKA 3DCMX 1VHYA 1UALA 5FAIA 3BBHA 3NK6A 1Z85A 4YVHA 2EGVA 3NK7A 2YY8A 4JAKA 3ILKA 3O7BA 4MCDA 4YQ6A 1MXIA 4CNDA 1IPAA 3IC6A 4YQKA 4JALA 4YVIA 1UAKA 4YQ1A 3GYQA 4YQ3A 4J3CA 3KW2A 4YQ0A 3AI9X 4RG1A 5D9FA 4YVKA 3E5YA 5GMCA 1ZJRA 4MCCA 3OIIA 4YPXA 4YQSA 3L8UA 2QMMA 4YQCA 4YQTA 4YQOA 4YQNA 4YQRA 4YQIA 3OIJA 4YQLA 4YQAA 4YQ2A 2HA8A 3N4JA 4YQBA 4YQ4A 4YQGA 4KGNA 4CNGA 1P9PA 4YQ9A 4H3YA 4YQPA 1NS5A 1VH0A 2V3KA 3IEFA 1UAMA 3AXZA 2EGWA 3KTYA 4PZKA 5GMBA 4YQ5A 4CNEA 3OINA 3KNUA 3AIAA 1X7OA 3BBEA 3ONPA 2O3AA 1X7PA 2CX8A 4MCBA 2I6DA 1K3RA 1V6ZA 4YQJA 1OY5A 3N4KA 4X3MA 5GM8A 4YQ7A 1J85A 4YQDA 3KY7A 4IG6A 5CO4A 4FAKA 2Z0YA 4YPYA 1O6DA 1V2XA 2V3JA 4L69A 4CNFA 4YVJA 1NXZA 1UAJA 1TO0A
chains in the Genus database with same CATH superfamily
2QWVA 4H3ZA 4YVGA 4YQQA 4YPZA 4YPWA 4E8BA 1GZ0A 4YQ8A 3QUVA 4KDZA 4X3LA 3BBDA 4XBOA 1VHKA 3DCMX 1VHYA 1UALA 5FAIA 3BBHA 3NK6A 1Z85A 4YVHA 2EGVA 3NK7A 2YY8A 4JAKA 3ILKA 3O7BA 4MCDA 4YQ6A 1MXIA 4CNDA 1IPAA 3IC6A 4YQKA 4JALA 4YVIA 1UAKA 4YQ1A 3GYQA 4YQ3A 4J3CA 3KW2A 4YQ0A 4JWFA 3AI9X 4RG1A 5D9FA 4YVKA 3E5YA 5GMCA 1ZJRA 4MCCA 3OIIA 4YPXA 4YQSA 3L8UA 2QMMA 4YQCA 4YQTA 4YQOA 4YQNA 4YQRA 4FMWA 4YQIA 3OIJA 4JWGA 4YQLA 4YQAA 4YQ2A 2HA8A 3N4JA 4JWJA 4YQBA 4YQ4A 4YQGA 4KGNA 4CNGA 1P9PA 4YQ9A 4H3YA 4YQPA 1NS5A 1VH0A 2V3KA 3IEFA 1UAMA 3AXZA 2EGWA 3KTYA 4PZKA 5GMBA 4YQ5A 4CNEA 3OINA 3KNUA 3AIAA 1X7OA 3BBEA 3ONPA 2O3AA 1X7PA 2CX8A 4MCBA 2I6DA 1K3RA 1V6ZA 4YQJA 1OY5A 3N4KA 4X3MA 5GM8A 4YQ7A 1J85A 4YQDA 3KY7A 4IG6A 5CO4A 4FAKA 2Z0YA 4YPYA 1O6DA 1V2XA 2V3JA 4L69A 4CNFA 4YVJA 1NXZA 1UAJA 1TO0A 4JWHA
chains in the Genus database with same CATH topology
2QWVA 4H3ZA 4YVGA 4YQQA 4YPZA 4YPWA 4E8BA 1GZ0A 4YQ8A 3QUVA 4KDZA 4X3LA 3BBDA 4XBOA 1VHKA 3DCMX 1VHYA 1UALA 5FAIA 3BBHA 3NK6A 1Z85A 4YVHA 2EGVA 3NK7A 2YY8A 4JAKA 3ILKA 3O7BA 4MCDA 4YQ6A 1MXIA 4CNDA 1IPAA 3IC6A 4YQKA 4JALA 4YVIA 1UAKA 4YQ1A 3GYQA 4YQ3A 4J3CA 3KW2A 4YQ0A 4JWFA 3AI9X 4RG1A 5D9FA 4YVKA 3E5YA 5GMCA 1ZJRA 4MCCA 3OIIA 4YPXA 4YQSA 3L8UA 2QMMA 4YQCA 4YQTA 4YQOA 4YQNA 4YQRA 4FMWA 4YQIA 3OIJA 4JWGA 4YQLA 4YQAA 4YQ2A 2HA8A 3N4JA 4JWJA 4YQBA 4YQ4A 4YQGA 4KGNA 4CNGA 1P9PA 4YQ9A 4H3YA 4YQPA 1NS5A 1VH0A 2V3KA 3IEFA 1UAMA 3AXZA 2EGWA 3KTYA 4PZKA 5GMBA 4YQ5A 4CNEA 3OINA 3KNUA 3AIAA 1X7OA 3BBEA 3ONPA 2O3AA 1X7PA 2CX8A 4MCBA 2I6DA 1K3RA 1V6ZA 4YQJA 1OY5A 3N4KA 4X3MA 5GM8A 4YQ7A 1J85A 4YQDA 3KY7A 4IG6A 5CO4A 4FAKA 2Z0YA 4YPYA 1O6DA 1V2XA 2V3JA 4L69A 4CNFA 4YVJA 1NXZA 1UAJA 1TO0A 4JWHA
chains in the Genus database with same CATH homology


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