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


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