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


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