4YQBA

Crystal structure of trmd, a m1g37 trna methyltransferase with sam-competitive compounds
Total Genus 72
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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
72
sequence length
248
structure length
240
Chain Sequence
GSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHN
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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/transferase inhibitor
molecule keywords tRNA (guanine-N(1)-)-methyltransferase
publication title Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
rcsb
source organism Haemophilus influenzae (strain atcc 51907 / dsm 11121 / kw20 / rd)
total genus 72
structure length 240
sequence length 248
ec nomenclature ec 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
pdb deposition date 2015-03-13

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01746 tRNA_m1G_MT tRNA (Guanine-1)-methyltransferase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.1270.20 Mainly Alpha Orthogonal Bundle Trp Operon Repressor; Chain A tRNA(m1g37)methyltransferase, domain 2 4yqbA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yqbA01
1IPAA 4YQOA 1V6ZA 3KW2A 4XBOA 4YPZA 4X3MA 1TO0A 3DCMX 4YPYA 2V3JA 1O6DA 5GMCA 4YQ9A 2I6DA 3N4JA 1J85A 4J3CA 4YQIA 1VH0A 2O3AA 1VHYA 4YQ4A 1VHKA 1V2XA 4RG1A 2V3KA 4YQLA 4H3ZA 4YVGA 3N4KA 5CO4A 4FAKA 3L8UA 4YQAA 4YQBA 3BBEA 4CNEA 4YQSA 3NK6A 3ONPA 2CX8A 1UALA 4YQKA 3BBHA 4X3LA 5FAIA 4YQCA 3KTYA 1UAKA 4JAKA 4JALA 4CNDA 3ILKA 4CNFA 1X7OA 4IG6A 4L69A 1UAJA 4YQ3A 3E5YA 4YQ1A 4YQTA 1X7PA 2HA8A 3QUVA 1GZ0A 3KY7A 2QMMA 4YQ6A 4YQDA 3OIJA 5D9FA 1Z85A 4YQ7A 1ZJRA 2Z0YA 3OINA 3OIIA 4YQQA 2EGWA 4MCCA 4YQPA 5GM8A 1MXIA 2EGVA 4MCDA 4YQ0A 2QWVA 4YQJA 4YVJA 4MCBA 3IEFA 3IC6A 1UAMA 3KNUA 4PZKA 1NXZA 4E8BA 1NS5A 4YPXA 4YVIA 3AI9X 4YVHA 3GYQA 3NK7A 4KGNA 3AIAA 4H3YA 4YQ5A 4YQGA 2YY8A 4KDZA 3BBDA 1OY5A 4YQNA 4YVKA 4YPWA 4YQ8A 4YQRA 4YQ2A 3O7BA 1P9PA 5GMBA 1K3RA 4CNGA 3AXZA
chains in the Genus database with same CATH superfamily
1IPAA 4YQOA 1V6ZA 3KW2A 4XBOA 4YPZA 3SSXN 4X3MA 1TO0A 3DCMX 4YPYA 3SSWN 2V3JA 1O6DA 5GMCA 4YQ9A 2I6DA 2OZ9R 1CO0A 3N4JA 3KORA 1J85A 4J3CA 4YQIA 1VH0A 4JWGA 2O3AA 1VHYA 4YQ4A 1VHKA 1V2XA 4FMWA 4RG1A 2V3KA 4YQLA 3FRWA 4YVGA 4H3ZA 3N4KA 5CO4A 4FAKA 3L8UA 4YQAA 4YQBA 3BBEA 4CNEA 4YQSA 3NK6A 3ONPA 2CX8A 1UALA 1TRRA 4YQKA 3BBHA 1JHGA 4X3LA 5FAIA 4YQCA 3KTYA 1UAKA 4JAKA 4JALA 4CNDA 3ILKA 4CNFA 1ZT9A 1X7OA 4IG6A 4L69A 1UAJA 4YQ3A 3E5YA 4YQ1A 4YQTA 1WRSR 1X7PA 2XDIA 2HA8A 3QUVA 1GZ0A 3KY7A 2QMMA 4YQ6A 4YQDA 3OIJA 5D9FA 1Z85A 4YQ7A 1ZJRA 2Z0YA 3OINA 3OIIA 4YQQA 2EGWA 4MCCA 4YQPA 5GM8A 1MXIA 2EGVA 4JWFA 4MCDA 4YQ0A 2QWVA 4YQJA 4YVJA 4MCBA 3IEFA 4JWHA 3IC6A 1UAMA 3KNUA 4PZKA 1NXZA 4E8BA 1NS5A 4YPXA 4YVIA 3AI9X 4YVHA 3GYQA 3NK7A 4KGNA 3AIAA 1TROA 4H3YA 4YQ5A 4YQGA 1MI7R 2YY8A 4KDZA 3BBDA 1OY5A 4YQNA 4YVKA 1WRPR 3G1CA 4YPWA 4YQ8A 4YQRA 4JWJA 4YQ2A 3WRPA 3O7BA 1P9PA 1RCSA 1K3RA 5GMBA 4CNGA 1WRTR 3AXZA
chains in the Genus database with same CATH topology
1IPAA 4YQOA 1V6ZA 3KW2A 4XBOA 4YPZA 4X3MA 1TO0A 3DCMX 4YPYA 2V3JA 1O6DA 5GMCA 4YQ9A 2I6DA 3N4JA 1J85A 4J3CA 4YQIA 1VH0A 4JWGA 2O3AA 1VHYA 4YQ4A 1VHKA 1V2XA 4FMWA 4RG1A 2V3KA 4YQLA 4H3ZA 4YVGA 3N4KA 5CO4A 4FAKA 3L8UA 4YQAA 4YQBA 3BBEA 4CNEA 4YQSA 3NK6A 3ONPA 2CX8A 1UALA 4YQKA 3BBHA 4X3LA 5FAIA 4YQCA 3KTYA 1UAKA 4JAKA 4JALA 4CNDA 3ILKA 4CNFA 1X7OA 4IG6A 4L69A 1UAJA 4YQ3A 3E5YA 4YQ1A 4YQTA 1X7PA 2HA8A 3QUVA 1GZ0A 3KY7A 2QMMA 4YQ6A 4YQDA 3OIJA 5D9FA 1Z85A 4YQ7A 1ZJRA 2Z0YA 3OINA 3OIIA 4YQQA 2EGWA 4MCCA 4YQPA 5GM8A 1MXIA 2EGVA 4JWFA 4MCDA 4YQ0A 2QWVA 4YQJA 4YVJA 4MCBA 3IEFA 4JWHA 3IC6A 1UAMA 3KNUA 4PZKA 1NXZA 4E8BA 1NS5A 4YPXA 4YVIA 3AI9X 4YVHA 3GYQA 3NK7A 4KGNA 3AIAA 4H3YA 4YQ5A 4YQGA 2YY8A 4KDZA 3BBDA 1OY5A 4YQNA 4YVKA 4YPWA 4YQ8A 4YQRA 4JWJA 4YQ2A 3O7BA 1P9PA 5GMBA 1K3RA 4CNGA 3AXZA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1IPA A;  4YQO A;  1V6Z A;  3KW2 A;  4XBO A;  4YPZ A;  4X3M A;  1TO0 A;  3DCM X;  4YPY A;  2V3J A;  1O6D A;  5GMC A;  4YQ9 A;  2I6D A;  3N4J A;  1J85 A;  4J3C A;  4YQI A;  1VH0 A;  2O3A A;  1VHY A;  4YQ4 A;  1VHK A;  1V2X A;  4RG1 A;  2V3K A;  4YQL A;  4H3Z A;  4YVG A;  3N4K A;  5CO4 A;  4FAK A;  3L8U A;  4YQA A;  4YQB A;  3BBE A;  4CNE A;  4YQS A;  3NK6 A;  3ONP A;  2CX8 A;  1UAL A;  4YQK A;  3BBH A;  4X3L A;  5FAI A;  4YQC A;  3KTY A;  1UAK A;  4JAK A;  4JAL A;  4CND A;  3ILK A;  4CNF A;  1X7O A;  4IG6 A;  4L69 A;  1UAJ A;  4YQ3 A;  3E5Y A;  4YQ1 A;  4YQT A;  1X7P A;  2HA8 A;  3QUV A;  1GZ0 A;  3KY7 A;  2QMM A;  4YQ6 A;  4YQD A;  3OIJ A;  5D9F A;  1Z85 A;  4YQ7 A;  1ZJR A;  2Z0Y A;  3OIN A;  3OII A;  4YQQ A;  2EGW A;  4MCC A;  4YQP A;  5GM8 A;  1MXI A;  2EGV A;  4MCD A;  4YQ0 A;  2QWV A;  4YQJ A;  4YVJ A;  4MCB A;  3IEF A;  3IC6 A;  1UAM A;  3KNU A;  4PZK A;  1NXZ A;  4E8B A;  1NS5 A;  4YPX A;  4YVI A;  3AI9 X;  4YVH A;  3GYQ A;  3NK7 A;  4KGN A;  3AIA A;  4H3Y A;  4YQ5 A;  4YQG A;  2YY8 A;  4KDZ A;  3BBD A;  1OY5 A;  4YQN A;  4YVK A;  4YPW A;  4YQ8 A;  4YQR A;  4YQ2 A;  3O7B A;  1P9P A;  5GMB A;  1K3R A;  4CNG A;  3AXZ A; 
#chains in the Genus database with same CATH topology
 1IPA A;  4YQO A;  1V6Z A;  3KW2 A;  4XBO A;  4YPZ A;  3SSX N;  4X3M A;  1TO0 A;  3DCM X;  4YPY A;  3SSW N;  2V3J A;  1O6D A;  5GMC A;  4YQ9 A;  2I6D A;  2OZ9 R;  1CO0 A;  3N4J A;  3KOR A;  1J85 A;  4J3C A;  4YQI A;  1VH0 A;  4JWG A;  2O3A A;  1VHY A;  4YQ4 A;  1VHK A;  1V2X A;  4FMW A;  4RG1 A;  2V3K A;  4YQL A;  3FRW A;  4YVG A;  4H3Z A;  3N4K A;  5CO4 A;  4FAK A;  3L8U A;  4YQA A;  4YQB A;  3BBE A;  4CNE A;  4YQS A;  3NK6 A;  3ONP A;  2CX8 A;  1UAL A;  1TRR A;  4YQK A;  3BBH A;  1JHG A;  4X3L A;  5FAI A;  4YQC A;  3KTY A;  1UAK A;  4JAK A;  4JAL A;  4CND A;  3ILK A;  4CNF A;  1ZT9 A;  1X7O A;  4IG6 A;  4L69 A;  1UAJ A;  4YQ3 A;  3E5Y A;  4YQ1 A;  4YQT A;  1WRS R;  1X7P A;  2XDI A;  2HA8 A;  3QUV A;  1GZ0 A;  3KY7 A;  2QMM A;  4YQ6 A;  4YQD A;  3OIJ A;  5D9F A;  1Z85 A;  4YQ7 A;  1ZJR A;  2Z0Y A;  3OIN A;  3OII A;  4YQQ A;  2EGW A;  4MCC A;  4YQP A;  5GM8 A;  1MXI A;  2EGV A;  4JWF A;  4MCD A;  4YQ0 A;  2QWV A;  4YQJ A;  4YVJ A;  4MCB A;  3IEF A;  4JWH A;  3IC6 A;  1UAM A;  3KNU A;  4PZK A;  1NXZ A;  4E8B A;  1NS5 A;  4YPX A;  4YVI A;  3AI9 X;  4YVH A;  3GYQ A;  3NK7 A;  4KGN A;  3AIA A;  1TRO A;  4H3Y A;  4YQ5 A;  4YQG A;  1MI7 R;  2YY8 A;  4KDZ A;  3BBD A;  1OY5 A;  4YQN A;  4YVK A;  1WRP R;  3G1C A;  4YPW A;  4YQ8 A;  4YQR A;  4JWJ A;  4YQ2 A;  3WRP A;  3O7B A;  1P9P A;  1RCS A;  1K3R A;  5GMB A;  4CNG A;  1WRT R;  3AXZ A; 
#chains in the Genus database with same CATH homology
 1IPA A;  4YQO A;  1V6Z A;  3KW2 A;  4XBO A;  4YPZ A;  4X3M A;  1TO0 A;  3DCM X;  4YPY A;  2V3J A;  1O6D A;  5GMC A;  4YQ9 A;  2I6D A;  3N4J A;  1J85 A;  4J3C A;  4YQI A;  1VH0 A;  4JWG A;  2O3A A;  1VHY A;  4YQ4 A;  1VHK A;  1V2X A;  4FMW A;  4RG1 A;  2V3K A;  4YQL A;  4H3Z A;  4YVG A;  3N4K A;  5CO4 A;  4FAK A;  3L8U A;  4YQA A;  4YQB A;  3BBE A;  4CNE A;  4YQS A;  3NK6 A;  3ONP A;  2CX8 A;  1UAL A;  4YQK A;  3BBH A;  4X3L A;  5FAI A;  4YQC A;  3KTY A;  1UAK A;  4JAK A;  4JAL A;  4CND A;  3ILK A;  4CNF A;  1X7O A;  4IG6 A;  4L69 A;  1UAJ A;  4YQ3 A;  3E5Y A;  4YQ1 A;  4YQT A;  1X7P A;  2HA8 A;  3QUV A;  1GZ0 A;  3KY7 A;  2QMM A;  4YQ6 A;  4YQD A;  3OIJ A;  5D9F A;  1Z85 A;  4YQ7 A;  1ZJR A;  2Z0Y A;  3OIN A;  3OII A;  4YQQ A;  2EGW A;  4MCC A;  4YQP A;  5GM8 A;  1MXI A;  2EGV A;  4JWF A;  4MCD A;  4YQ0 A;  2QWV A;  4YQJ A;  4YVJ A;  4MCB A;  3IEF A;  4JWH A;  3IC6 A;  1UAM A;  3KNU A;  4PZK A;  1NXZ A;  4E8B A;  1NS5 A;  4YPX A;  4YVI A;  3AI9 X;  4YVH A;  3GYQ A;  3NK7 A;  4KGN A;  3AIA A;  4H3Y A;  4YQ5 A;  4YQG A;  2YY8 A;  4KDZ A;  3BBD A;  1OY5 A;  4YQN A;  4YVK A;  4YPW A;  4YQ8 A;  4YQR A;  4JWJ A;  4YQ2 A;  3O7B A;  1P9P A;  5GMB A;  1K3R A;  4CNG A;  3AXZ 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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