5GM8A

Methylation at position 32 of trna catalyzed by trmj alters oxidative stress response in pseudomonas aeruiginosa
Total Genus 60
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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
60
Knots found
sequence length
170
structure length
170
Chain Sequence
QSMMLDRIRVVLVNTSHPGNIGGAARAMKNMGLSQLVLVQPESFPHGDAVARASGATDILDAARVVDTLEEALSGCSVVLGTSARDRRIPWPLLDPRECATTCLEHLEANGEVALVFGREYAGLTNEELQRCQFHVHIPSDPEFGSLNLAAAVQVLTYEVRMAWLAAQGK
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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 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ
publication title Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa.
pubmed doi rcsb
source organism Pseudomonas aeruginosa
total genus 60
structure length 170
sequence length 170
chains with identical sequence B, C, D
other databases KnotProt 2.0: K +31
ec nomenclature ec 2.1.1.200: tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase.
pdb deposition date 2016-07-13

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00588 SpoU_methylase SpoU rRNA Methylase family
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 5gm8A01
4MCDA 4YQ7A 2O3AA 3E5YA 4YQ0A 4CNFA 4YQ9A 1P9PA 1UALA 2YY8A 4YQCA 4YQPA 3AXZA 4YQRA 5GMCA 3ILKA 3NK6A 4YPWA 2Z0YA 1UAMA 4YPXA 4YQTA 3GYQA 1IPAA 4YQJA 3KNUA 4H3YA 2V3KA 4IG6A 4YQKA 5D9FA 4YQBA 5FAIA 1K3RA 4YQ1A 1O6DA 2CX8A 1Z85A 2I6DA 3OIJA 4YVGA 3IEFA 4YVJA 2QWVA 4KGNA 5CO4A 3O7BA 1ZJRA 4RG1A 4X3MA 5GM8A 4YQQA 4YQOA 4YPZA 1UAKA 3BBDA 1VHYA 3N4KA 4YVHA 1X7OA 3KTYA 1NS5A 4J3CA 4YQGA 1NXZA 3AI9X 4E8BA 3BBHA 1V6ZA 4YQNA 4YQLA 4YQIA 4KDZA 4YQ6A 1GZ0A 4MCBA 4MCCA 4YQDA 1MXIA 4YQ4A 4FAKA 2EGWA 1X7PA 3QUVA 1OY5A 3OIIA 4PZKA 1V2XA 4CNGA 2EGVA 4YVIA 4YQSA 3AIAA 2QMMA 1VHKA 4YQ8A 3N4JA 3NK7A 4JAKA 2HA8A 4CNEA 4XBOA 3DCMX 4YVKA 1TO0A 5GMBA 3KW2A 4YQ3A 4H3ZA 3KY7A 3IC6A 4CNDA 4YQAA 4YPYA 2V3JA 1VH0A 1J85A 3OINA 3L8UA 1UAJA 4L69A 4YQ2A 4JALA 3BBEA 3ONPA 4X3LA 4YQ5A
chains in the Genus database with same CATH superfamily
4MCDA 4YQ7A 2O3AA 3E5YA 4YQ0A 4CNFA 4YQ9A 1P9PA 1UALA 2YY8A 4YQCA 4YQPA 3AXZA 4YQRA 4FMWA 5GMCA 4JWJA 3ILKA 3NK6A 4JWGA 4YPWA 2Z0YA 1UAMA 4YPXA 4YQTA 3GYQA 1IPAA 4YQJA 3KNUA 4H3YA 2V3KA 4IG6A 4YQKA 5D9FA 4YQBA 5FAIA 1K3RA 4YQ1A 1O6DA 2CX8A 1Z85A 2I6DA 3OIJA 4YVGA 3IEFA 4YVJA 2QWVA 4KGNA 5CO4A 3O7BA 1ZJRA 4RG1A 4X3MA 5GM8A 4YQQA 4YQOA 4YPZA 1UAKA 3BBDA 1VHYA 3N4KA 4YVHA 1X7OA 3KTYA 1NS5A 4JWHA 4J3CA 4YQGA 1NXZA 3AI9X 4E8BA 3BBHA 1V6ZA 4YQNA 4YQLA 4YQIA 4KDZA 4YQ6A 1GZ0A 4MCBA 4MCCA 4YQDA 1MXIA 4YQ4A 4FAKA 2EGWA 1X7PA 3QUVA 1OY5A 3OIIA 4PZKA 1V2XA 4CNGA 2EGVA 4YVIA 4YQSA 3AIAA 2QMMA 1VHKA 4YQ8A 3N4JA 3NK7A 4JAKA 2HA8A 4CNEA 4XBOA 3DCMX 4YVKA 1TO0A 5GMBA 3KW2A 4YQ3A 4H3ZA 3KY7A 3IC6A 4CNDA 4YQAA 4YPYA 2V3JA 1VH0A 1J85A 3OINA 3L8UA 1UAJA 4L69A 4YQ2A 4JALA 3BBEA 4JWFA 3ONPA 4X3LA 4YQ5A
chains in the Genus database with same CATH topology
4MCDA 4YQ7A 2O3AA 3E5YA 4YQ0A 4CNFA 4YQ9A 1P9PA 1UALA 2YY8A 4YQCA 4YQPA 3AXZA 4YQRA 4FMWA 5GMCA 4JWJA 3ILKA 3NK6A 4JWGA 4YPWA 2Z0YA 1UAMA 4YPXA 4YQTA 3GYQA 1IPAA 4YQJA 3KNUA 4H3YA 2V3KA 4IG6A 4YQKA 5D9FA 4YQBA 5FAIA 1K3RA 4YQ1A 1O6DA 2CX8A 1Z85A 2I6DA 3OIJA 4YVGA 3IEFA 4YVJA 2QWVA 4KGNA 5CO4A 3O7BA 1ZJRA 4RG1A 4X3MA 5GM8A 4YQQA 4YQOA 4YPZA 1UAKA 3BBDA 1VHYA 3N4KA 4YVHA 1X7OA 3KTYA 1NS5A 4JWHA 4J3CA 4YQGA 1NXZA 3AI9X 4E8BA 3BBHA 1V6ZA 4YQNA 4YQLA 4YQIA 4KDZA 4YQ6A 1GZ0A 4MCBA 4MCCA 4YQDA 1MXIA 4YQ4A 4FAKA 2EGWA 1X7PA 3QUVA 1OY5A 3OIIA 4PZKA 1V2XA 4CNGA 2EGVA 4YVIA 4YQSA 3AIAA 2QMMA 1VHKA 4YQ8A 3N4JA 3NK7A 4JAKA 2HA8A 4CNEA 4XBOA 3DCMX 4YVKA 1TO0A 5GMBA 3KW2A 4YQ3A 4H3ZA 3KY7A 3IC6A 4CNDA 4YQAA 4YPYA 2V3JA 1VH0A 1J85A 3OINA 3L8UA 1UAJA 4L69A 4YQ2A 4JALA 3BBEA 4JWFA 3ONPA 4X3LA 4YQ5A
chains in the Genus database with same CATH homology


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