4YPWA

Crystal structure of trmd, a m1g37 trna methyltransferase with sam-competitive compounds
Total Genus 67
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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
67
sequence length
249
structure length
238
Chain Sequence
GSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGDGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
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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 67
structure length 238
sequence length 249
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 4ypwA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4ypwA01
4IG6A 4YQQA 4L69A 2QWVA 1UAMA 3GYQA 3OINA 4YQ7A 4PZKA 5GM8A 4YQ9A 1O6DA 4YQ2A 4YQDA 3AIAA 4YQTA 4YVIA 2O3AA 4YQCA 4YVKA 4YQBA 4XBOA 4YPWA 1GZ0A 3BBDA 3L8UA 4J3CA 4JAKA 3E5YA 4YQ4A 3DCMX 5FAIA 3IEFA 3KY7A 4YQLA 1X7PA 4MCDA 4JALA 4YQRA 5GMCA 5D9FA 1VHYA 1IPAA 2Z0YA 4MCBA 4YQKA 2QMMA 4YQ0A 4YQNA 4E8BA 4X3LA 3KW2A 3BBEA 1P9PA 1Z85A 3O7BA 4FAKA 1VHKA 1X7OA 4RG1A 4YVHA 4YQ8A 2I6DA 3ONPA 4KGNA 4CNFA 3AI9X 3IC6A 1OY5A 3BBHA 4MCCA 1NS5A 1UAJA 3KTYA 4YQ5A 4YQ1A 3QUVA 4YQOA 5GMBA 4YQPA 2V3KA 1MXIA 2CX8A 3AXZA 4YQ3A 4YVGA 2V3JA 2EGWA 2HA8A 4CNEA 4X3MA 4YQJA 4YQSA 5CO4A 4H3YA 4H3ZA 1VH0A 3NK6A 4YQAA 1V6ZA 1V2XA 4CNDA 4YQ6A 3ILKA 4YPYA 1TO0A 1NXZA 4YPZA 3N4JA 3OIIA 3NK7A 4YPXA 3OIJA 1ZJRA 4YQIA 4YVJA 3N4KA 3KNUA 1J85A 2YY8A 1UALA 1K3RA 1UAKA 4CNGA 2EGVA 4YQGA 4KDZA
chains in the Genus database with same CATH superfamily
4IG6A 4YQQA 4JWGA 4L69A 3G1CA 1WRTR 2QWVA 1UAMA 3GYQA 3OINA 4YQ7A 4PZKA 1RCSA 5GM8A 4YQ9A 1O6DA 4YQ2A 4YQDA 3AIAA 4YQTA 4YVIA 2O3AA 4YQCA 1CO0A 4YVKA 4YQBA 4XBOA 4YPWA 2XDIA 1GZ0A 3BBDA 3L8UA 4J3CA 4JAKA 3E5YA 4YQ4A 3DCMX 5FAIA 3IEFA 3KY7A 4YQLA 1TROA 1X7PA 4MCDA 4JALA 4YQRA 5GMCA 5D9FA 3FRWA 1VHYA 1IPAA 2Z0YA 4MCBA 4YQKA 2QMMA 4YQ0A 4YQNA 4E8BA 2OZ9R 4JWFA 4X3LA 3KW2A 3BBEA 1P9PA 1WRPR 1Z85A 3O7BA 4FAKA 1VHKA 1X7OA 4RG1A 1ZT9A 4YVHA 4YQ8A 2I6DA 3ONPA 4KGNA 3SSXN 3SSWN 4CNFA 3AI9X 3IC6A 1OY5A 3WRPA 3BBHA 4MCCA 1NS5A 1UAJA 3KTYA 4YQ5A 4YQ1A 3QUVA 4YQOA 5GMBA 4JWHA 1JHGA 4YQPA 2V3KA 1MXIA 2CX8A 3AXZA 4YQ3A 4YVGA 2V3JA 2EGWA 2HA8A 4CNEA 4X3MA 4YQJA 4YQSA 5CO4A 1WRSR 4H3YA 4H3ZA 4JWJA 1VH0A 4FMWA 3NK6A 4YQAA 1V6ZA 3KORA 1V2XA 4CNDA 4YQ6A 3ILKA 4YPYA 1TO0A 1TRRA 4YPZA 1NXZA 3N4JA 3OIIA 3NK7A 4YPXA 3OIJA 1ZJRA 4YQIA 1MI7R 4YVJA 3N4KA 3KNUA 1J85A 2YY8A 1UALA 1K3RA 1UAKA 4CNGA 2EGVA 4YQGA 4KDZA
chains in the Genus database with same CATH topology
4IG6A 4YQQA 4JWGA 4L69A 2QWVA 1UAMA 3GYQA 3OINA 4YQ7A 4PZKA 5GM8A 4YQ9A 1O6DA 4YQ2A 4YQDA 3AIAA 4YQTA 4YVIA 2O3AA 4YQCA 4YVKA 4YQBA 4XBOA 4YPWA 1GZ0A 3BBDA 3L8UA 4J3CA 4JAKA 3E5YA 4YQ4A 3DCMX 5FAIA 3IEFA 3KY7A 4YQLA 1X7PA 4MCDA 4JALA 4YQRA 5GMCA 5D9FA 1VHYA 1IPAA 2Z0YA 4MCBA 4YQKA 2QMMA 4YQ0A 4YQNA 4E8BA 4JWFA 4X3LA 3KW2A 3BBEA 1P9PA 1Z85A 3O7BA 4FAKA 1VHKA 1X7OA 4RG1A 4YVHA 4YQ8A 2I6DA 3ONPA 4KGNA 4CNFA 3AI9X 3IC6A 1OY5A 3BBHA 4MCCA 1NS5A 1UAJA 3KTYA 4YQ5A 4YQ1A 3QUVA 4YQOA 5GMBA 4JWHA 4YQPA 2V3KA 1MXIA 2CX8A 3AXZA 4YQ3A 4YVGA 2V3JA 2EGWA 2HA8A 4CNEA 4X3MA 4YQJA 4YQSA 5CO4A 4H3YA 4H3ZA 4JWJA 1VH0A 4FMWA 3NK6A 4YQAA 1V6ZA 1V2XA 4CNDA 4YQ6A 3ILKA 4YPYA 1TO0A 1NXZA 4YPZA 3N4JA 3OIIA 3NK7A 4YPXA 3OIJA 1ZJRA 4YQIA 4YVJA 3N4KA 3KNUA 1J85A 2YY8A 1UALA 1K3RA 1UAKA 4CNGA 2EGVA 4YQGA 4KDZA
chains in the Genus database with same CATH homology


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