5GMCA

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
174
structure length
174
Chain Sequence
NLYFQSMMLDRIRVVLVNTSHPGNIGGAARAMKNMGLSQLVLVQPESFPHGDAVARASGATDILDAARVVDTLEEALSGCSVVLGTSARDRRIPWPLLDPRECATTCLEHLEANGEVALVFGREYAGLTNEELQRCQFHVHIPSDPEFGSLNLAAAVQVLTYEVRMAWLAAQGK
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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 60
structure length 174
sequence length 174
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 5gmcA01
3ONPA 4RG1A 3N4KA 2CX8A 4MCDA 4X3LA 1J85A 1VHKA 4YQGA 2EGVA 1OY5A 2EGWA 1UAKA 4J3CA 3KTYA 5GMCA 4YVIA 3GYQA 3KW2A 4YPZA 1IPAA 4XBOA 4CNFA 4YQ9A 3NK7A 3AIAA 4YPXA 3QUVA 1V6ZA 1VHYA 1X7PA 1O6DA 4H3YA 1VH0A 4JALA 4MCCA 3BBDA 4CNDA 4CNGA 4E8BA 4MCBA 4YQ3A 4PZKA 4YQQA 4KGNA 3KNUA 4YQSA 4YQDA 1P9PA 3AI9X 4H3ZA 3DCMX 4YQKA 2YY8A 2HA8A 3BBHA 4YQOA 2V3JA 3OIJA 5GMBA 4YPYA 1UALA 3OINA 1NS5A 5D9FA 3N4JA 4YVGA 4YQ8A 1X7OA 3BBEA 1V2XA 3NK6A 4CNEA 4YQ6A 1ZJRA 4FAKA 4YQ7A 4YQ0A 3AXZA 4IG6A 1GZ0A 4YPWA 4YQ4A 2QWVA 1MXIA 3IC6A 1UAMA 4YQLA 4YQNA 1NXZA 4JAKA 4YQJA 2Z0YA 4YQ5A 1K3RA 4L69A 2V3KA 4KDZA 4YQIA 1TO0A 3KY7A 3OIIA 1UAJA 5CO4A 3L8UA 4YQCA 3IEFA 4YQPA 4YVJA 1Z85A 2I6DA 4YQRA 4YVHA 4YQTA 3E5YA 4YQ2A 4YVKA 3ILKA 2O3AA 2QMMA 4YQBA 5FAIA 4YQ1A 4X3MA 5GM8A 3O7BA 4YQAA
chains in the Genus database with same CATH superfamily
3ONPA 4RG1A 3N4KA 2CX8A 4MCDA 4X3LA 1J85A 1VHKA 4YQGA 2EGVA 1OY5A 2EGWA 1UAKA 4JWHA 4J3CA 3KTYA 5GMCA 4YVIA 3GYQA 3KW2A 4YPZA 1IPAA 4XBOA 4CNFA 4YQ9A 4FMWA 3NK7A 3AIAA 4YPXA 3QUVA 1V6ZA 1VHYA 1X7PA 1O6DA 4H3YA 1VH0A 4JALA 4MCCA 3BBDA 4CNDA 4CNGA 4E8BA 4MCBA 4YQ3A 4PZKA 4YQQA 4KGNA 3KNUA 4YQSA 4YQDA 1P9PA 3AI9X 4H3ZA 3DCMX 4YQKA 2YY8A 4JWFA 2HA8A 3BBHA 4YQOA 2V3JA 3OIJA 4JWGA 5GMBA 4YPYA 1UALA 3OINA 1NS5A 5D9FA 3N4JA 4YVGA 4YQ8A 1X7OA 3BBEA 1V2XA 3NK6A 4CNEA 4YQ6A 1ZJRA 4FAKA 4YQ7A 4YQ0A 3AXZA 4JWJA 4IG6A 1GZ0A 4YPWA 4YQ4A 2QWVA 1MXIA 3IC6A 1UAMA 4YQLA 4YQNA 1NXZA 4JAKA 4YQJA 2Z0YA 4YQ5A 1K3RA 4L69A 2V3KA 4KDZA 4YQIA 1TO0A 3KY7A 3OIIA 1UAJA 5CO4A 3L8UA 4YQCA 3IEFA 4YQPA 4YVJA 1Z85A 2I6DA 4YQRA 4YVHA 4YQTA 3E5YA 4YQ2A 4YVKA 3ILKA 2O3AA 2QMMA 4YQBA 5FAIA 4YQ1A 4X3MA 5GM8A 3O7BA 4YQAA
chains in the Genus database with same CATH topology
3ONPA 4RG1A 3N4KA 2CX8A 4MCDA 4X3LA 1J85A 1VHKA 4YQGA 2EGVA 1OY5A 2EGWA 1UAKA 4JWHA 4J3CA 3KTYA 5GMCA 4YVIA 3GYQA 3KW2A 4YPZA 1IPAA 4XBOA 4CNFA 4YQ9A 4FMWA 3NK7A 3AIAA 4YPXA 3QUVA 1V6ZA 1VHYA 1X7PA 1O6DA 4H3YA 1VH0A 4JALA 4MCCA 3BBDA 4CNDA 4CNGA 4E8BA 4MCBA 4YQ3A 4PZKA 4YQQA 4KGNA 3KNUA 4YQSA 4YQDA 1P9PA 3AI9X 4H3ZA 3DCMX 4YQKA 2YY8A 4JWFA 2HA8A 3BBHA 4YQOA 2V3JA 3OIJA 4JWGA 5GMBA 4YPYA 1UALA 3OINA 1NS5A 5D9FA 3N4JA 4YVGA 4YQ8A 1X7OA 3BBEA 1V2XA 3NK6A 4CNEA 4YQ6A 1ZJRA 4FAKA 4YQ7A 4YQ0A 3AXZA 4JWJA 4IG6A 1GZ0A 4YPWA 4YQ4A 2QWVA 1MXIA 3IC6A 1UAMA 4YQLA 4YQNA 1NXZA 4JAKA 4YQJA 2Z0YA 4YQ5A 1K3RA 4L69A 2V3KA 4KDZA 4YQIA 1TO0A 3KY7A 3OIIA 1UAJA 5CO4A 3L8UA 4YQCA 3IEFA 4YQPA 4YVJA 1Z85A 2I6DA 4YQRA 4YVHA 4YQTA 3E5YA 4YQ2A 4YVKA 3ILKA 2O3AA 2QMMA 4YQBA 5FAIA 4YQ1A 4X3MA 5GM8A 3O7BA 4YQAA
chains in the Genus database with same CATH homology


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