5GMBA

Methylation at position 32 of trna catalyzed by trmj alters oxidative stress response in pseudomonas aeruiginosa
Total Genus 68
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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
68
Knots found
sequence length
171
structure length
171
Chain Sequence
b'FQSMMLDRIRVVLVNTSHPGNIGGAARAMKNMGLSQLVLVQPESFPHGDAVARASGATDILDAARVVDTLEEALSGCSVVLGTSARDRRIPWPLLDPRECATTCLEHLEANGEVALVFGREYAGLTNEELQRCQFHVHIPSDPEFGSLNLAAAVQVLTYEVRMAWLAAQGK'
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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 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
molecule tags Transferase
total genus 68
structure length 171
sequence length 171
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 5gmbA01
1NS5A 3OIJA 4CNFA 2Z0YA 3BBEA 3IEFA 4YQ5A 4YQ1A 4X3LA 4YQJA 4YQTA 1J85A 1UALA 3N4JA 3KY7A 4YVHA 4JALA 4YQ8A 1O6DA 3OINA 1OY5A 1V2XA 4YQSA 5D9FA 4YQ2A 4J3CA 4RG1A 4JAKA 4MCCA 4YQ3A 3KTYA 4YQDA 4YPZA 4YVJA 2EGVA 4YQIA 4YPXA 2CX8A 1IPAA 1X7OA 3L8UA 1NXZA 4YQLA 4YPWA 1VH0A 1TO0A 2YY8A 4YPYA 4YQ4A 4YVGA 3N4KA 3NK6A 4YQOA 3BBHA 2V3KA 3O7BA 5CO4A 1UAMA 4MCBA 4YQCA 4CNEA 4YQ6A 1X7PA 4IG6A 4YQ7A 5GM8A 2QMMA 4YQQA 4L69A 4YQGA 1ZJRA 3AXZA 2HA8A 4PZKA 4H3ZA 4YQ9A 1GZ0A 4YQRA 1Z85A 4MCDA 4E8BA 3KW2A 4CNDA 3OIIA 1MXIA 4YQAA 4KGNA 3ILKA 3NK7A 1VHKA 5FAIA 2QWVA 1V6ZA 5GMBA 4YVKA 4YQNA 4KDZA 4YQBA 4YQKA 2O3AA 3QUVA 1UAKA 4X3MA 1P9PA 3ONPA 4FAKA 3GYQA 4YVIA 3IC6A 3BBDA 3AI9X 3KNUA 3DCMX 1UAJA 4YQ0A 2V3JA 5GMCA 3E5YA 4YQPA 4H3YA 1K3RA 3AIAA 4CNGA 4XBOA 2I6DA 2EGWA 1VHYA
chains in the Genus database with same CATH superfamily
1NS5A 3OIJA 4CNFA 2Z0YA 3BBEA 3IEFA 4YQ5A 4YQ1A 4X3LA 4YQJA 4YQTA 1J85A 1UALA 3N4JA 3KY7A 4YVHA 4JALA 4YQ8A 1O6DA 3OINA 1OY5A 1V2XA 4YQSA 5D9FA 4YQ2A 4J3CA 4RG1A 4JAKA 4MCCA 4YQ3A 3KTYA 4YQDA 4YPZA 4YVJA 2EGVA 4YQIA 4JWHA 4YPXA 2CX8A 1IPAA 1X7OA 3L8UA 1NXZA 4YQLA 4YPWA 1VH0A 1TO0A 2YY8A 4YPYA 4YQ4A 4YVGA 3N4KA 3NK6A 4YQOA 3BBHA 2V3KA 3O7BA 5CO4A 1UAMA 4MCBA 4JWFA 4YQCA 4CNEA 4YQ6A 1X7PA 4IG6A 4YQ7A 4JWGA 5GM8A 2QMMA 4YQQA 4L69A 4YQGA 1ZJRA 3AXZA 2HA8A 4PZKA 4H3ZA 4YQ9A 1GZ0A 4YQRA 1Z85A 4MCDA 4E8BA 3KW2A 4CNDA 3OIIA 1MXIA 4YQAA 4KGNA 3ILKA 3NK7A 1VHKA 5FAIA 2QWVA 1V6ZA 5GMBA 4YVKA 4YQNA 4KDZA 4YQBA 4YQKA 2O3AA 3QUVA 1UAKA 4X3MA 1P9PA 3ONPA 4FAKA 3GYQA 4FMWA 4YVIA 3IC6A 3BBDA 3AI9X 3KNUA 3DCMX 1UAJA 4YQ0A 2V3JA 5GMCA 3E5YA 4YQPA 4H3YA 1K3RA 3AIAA 4CNGA 4XBOA 2I6DA 4JWJA 2EGWA 1VHYA
chains in the Genus database with same CATH topology
1NS5A 3OIJA 4CNFA 2Z0YA 3BBEA 3IEFA 4YQ5A 4YQ1A 4X3LA 4YQJA 4YQTA 1J85A 1UALA 3N4JA 3KY7A 4YVHA 4JALA 4YQ8A 1O6DA 3OINA 1OY5A 1V2XA 4YQSA 5D9FA 4YQ2A 4J3CA 4RG1A 4JAKA 4MCCA 4YQ3A 3KTYA 4YQDA 4YPZA 4YVJA 2EGVA 4YQIA 4JWHA 4YPXA 2CX8A 1IPAA 1X7OA 3L8UA 1NXZA 4YQLA 4YPWA 1VH0A 1TO0A 2YY8A 4YPYA 4YQ4A 4YVGA 3N4KA 3NK6A 4YQOA 3BBHA 2V3KA 3O7BA 5CO4A 1UAMA 4MCBA 4JWFA 4YQCA 4CNEA 4YQ6A 1X7PA 4IG6A 4YQ7A 4JWGA 5GM8A 2QMMA 4YQQA 4L69A 4YQGA 1ZJRA 3AXZA 2HA8A 4PZKA 4H3ZA 4YQ9A 1GZ0A 4YQRA 1Z85A 4MCDA 4E8BA 3KW2A 4CNDA 3OIIA 1MXIA 4YQAA 4KGNA 3ILKA 3NK7A 1VHKA 5FAIA 2QWVA 1V6ZA 5GMBA 4YVKA 4YQNA 4KDZA 4YQBA 4YQKA 2O3AA 3QUVA 1UAKA 4X3MA 1P9PA 3ONPA 4FAKA 3GYQA 4FMWA 4YVIA 3IC6A 3BBDA 3AI9X 3KNUA 3DCMX 1UAJA 4YQ0A 2V3JA 5GMCA 3E5YA 4YQPA 4H3YA 1K3RA 3AIAA 4CNGA 4XBOA 2I6DA 4JWJA 2EGWA 1VHYA
chains in the Genus database with same CATH homology


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