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


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