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


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