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


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