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


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

 
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#similar chains, but unknotted
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