5D9FA

Crystal structure of trmd, a m1g37 trna methyltransferase with sam-competitive compounds
Total Genus 69
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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
69
sequence length
248
structure length
237
Chain Sequence
GSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGDGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHN
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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
total genus 69
structure length 237
sequence length 248
ec nomenclature ec 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
pdb deposition date 2015-08-18

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 5d9fA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 5d9fA01
1Z85A 1VHKA 4YVIA 4YQOA 4YQKA 4YQDA 1X7OA 4KGNA 4X3MA 3N4KA 4YQRA 3N4JA 4YPWA 4FAKA 3OIIA 4YQ0A 4YQNA 4YQQA 4YPXA 5CO4A 4H3ZA 4YPZA 3KTYA 3KW2A 1O6DA 5GM8A 4YQ6A 4YQCA 1V2XA 3IEFA 1UAJA 4JALA 3KY7A 4L69A 3DCMX 4YQ1A 1UALA 4CNDA 1X7PA 1UAKA 4YQSA 4YVHA 2EGWA 4IG6A 4X3LA 1TO0A 1VHYA 4YQ2A 3NK6A 5GMCA 2QWVA 4H3YA 3OINA 2YY8A 4JAKA 3AXZA 4YQ5A 1NXZA 4YQ3A 4XBOA 4YQGA 3AIAA 2V3KA 4CNFA 4YPYA 2EGVA 1V6ZA 2CX8A 3IC6A 3ILKA 3BBEA 1OY5A 2O3AA 1K3RA 4RG1A 4CNEA 4YQ8A 4YQ7A 3ONPA 4YQBA 4YVKA 1UAMA 4CNGA 4YQ4A 2QMMA 3GYQA 4YQTA 2HA8A 1GZ0A 4YVJA 3L8UA 3KNUA 4PZKA 3AI9X 3O7BA 1IPAA 4E8BA 2V3JA 3BBDA 2I6DA 5D9FA 5FAIA 4J3CA 1MXIA 4YQJA 3OIJA 4MCDA 5GMBA 4YQPA 3QUVA 1P9PA 4YVGA 4YQ9A 1NS5A 3BBHA 4KDZA 4YQIA 4YQAA 4MCBA 1ZJRA 3NK7A 1J85A 4YQLA 2Z0YA 3E5YA 4MCCA 1VH0A
chains in the Genus database with same CATH superfamily
1Z85A 1VHKA 4YVIA 3SSXN 4YQOA 4YQKA 4JWGA 1JHGA 4YQDA 1ZT9A 1X7OA 4KGNA 4X3MA 3N4KA 4YQRA 3N4JA 4YPWA 4FAKA 3OIIA 4YQ0A 4YQNA 4YQQA 4YPXA 5CO4A 4H3ZA 4YPZA 3KTYA 3KW2A 1O6DA 5GM8A 4YQ6A 4YQCA 1V2XA 3SSWN 3IEFA 1UAJA 4JALA 3KY7A 1RCSA 3DCMX 4L69A 4YQ1A 1UALA 4CNDA 1TROA 1UAKA 1X7PA 4YQSA 4YVHA 2EGWA 4IG6A 4X3LA 1TO0A 1VHYA 1WRTR 4YQ2A 3NK6A 1WRSR 5GMCA 2QWVA 1WRPR 4H3YA 3OINA 4JWHA 2YY8A 4JAKA 2OZ9R 3AXZA 4YQ5A 1NXZA 4YQ3A 4XBOA 4YQGA 3AIAA 2V3KA 4CNFA 4YPYA 2EGVA 1V6ZA 2CX8A 3IC6A 3ILKA 3BBEA 4JWJA 1OY5A 2O3AA 1K3RA 4RG1A 4CNEA 4YQ8A 4YQ7A 3ONPA 4YQBA 3G1CA 4YVKA 1UAMA 4CNGA 4YQ4A 2QMMA 3FRWA 3GYQA 4YQTA 2HA8A 1TRRA 1GZ0A 4YVJA 3L8UA 3KNUA 4PZKA 1CO0A 3AI9X 4FMWA 3O7BA 1MI7R 1IPAA 4E8BA 2V3JA 4JWFA 3WRPA 3BBDA 2I6DA 5D9FA 5FAIA 4J3CA 1MXIA 4YQJA 3OIJA 4MCDA 5GMBA 4YQPA 3QUVA 1P9PA 4YVGA 4YQ9A 1NS5A 3BBHA 4KDZA 4YQIA 4YQAA 4MCBA 1ZJRA 3KORA 2XDIA 3NK7A 1J85A 4YQLA 2Z0YA 3E5YA 4MCCA 1VH0A
chains in the Genus database with same CATH topology
1Z85A 1VHKA 4YVIA 4YQOA 4YQKA 4JWGA 4YQDA 1X7OA 4KGNA 4X3MA 3N4KA 4YQRA 3N4JA 4YPWA 4FAKA 3OIIA 4YQ0A 4YQNA 4YQQA 4YPXA 5CO4A 4H3ZA 4YPZA 3KTYA 3KW2A 1O6DA 5GM8A 4YQ6A 4YQCA 1V2XA 3IEFA 1UAJA 4JALA 3KY7A 4L69A 3DCMX 4YQ1A 1UALA 4CNDA 1X7PA 1UAKA 4YQSA 4YVHA 2EGWA 4IG6A 4X3LA 1TO0A 1VHYA 4YQ2A 3NK6A 5GMCA 2QWVA 4H3YA 3OINA 4JWHA 2YY8A 4JAKA 3AXZA 4YQ5A 1NXZA 4YQ3A 4XBOA 4YQGA 3AIAA 2V3KA 4CNFA 4YPYA 2EGVA 1V6ZA 2CX8A 3IC6A 3ILKA 3BBEA 4JWJA 1OY5A 2O3AA 1K3RA 4RG1A 4CNEA 4YQ8A 4YQ7A 3ONPA 4YQBA 4YVKA 1UAMA 4CNGA 4YQ4A 2QMMA 3GYQA 4YQTA 2HA8A 1GZ0A 4YVJA 3L8UA 3KNUA 4PZKA 3AI9X 4FMWA 3O7BA 1IPAA 4E8BA 2V3JA 4JWFA 3BBDA 2I6DA 5D9FA 5FAIA 4J3CA 1MXIA 4YQJA 3OIJA 4MCDA 5GMBA 4YQPA 3QUVA 1P9PA 4YVGA 4YQ9A 1NS5A 3BBHA 4KDZA 4YQIA 4YQAA 4MCBA 1ZJRA 3NK7A 1J85A 4YQLA 2Z0YA 3E5YA 4MCCA 1VH0A
chains in the Genus database with same CATH homology


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