4YQ5A

Crystal structure of trmd, a m1g37 trna methyltransferase with sam-competitive compounds
Total Genus 74
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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
74
sequence length
253
structure length
244
Chain Sequence
LVPRGSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
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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 74
structure length 244
sequence length 253
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 4yq5A02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yq5A01
4YQKA 3BBEA 1VHKA 3N4KA 2EGVA 2O3AA 4X3MA 1K3RA 4YQQA 1UALA 3KTYA 4YQAA 3KNUA 1X7OA 2EGWA 4CNGA 3KW2A 4YPXA 3NK7A 2QWVA 1V6ZA 4YQOA 5GM8A 1Z85A 4YQTA 4YQLA 3OIJA 1UAJA 4YPYA 1VH0A 2QMMA 3AI9X 1O6DA 3L8UA 4YQBA 1IPAA 4FAKA 4YQ2A 5FAIA 4X3LA 2HA8A 4JAKA 3AIAA 1UAKA 4YQ7A 4MCDA 4YQIA 4YVIA 1X7PA 3ONPA 4YQ8A 4YQCA 4KDZA 2I6DA 3OINA 4YVGA 3E5YA 3AXZA 1OY5A 4CNDA 1ZJRA 4YQDA 1VHYA 4YQ9A 1MXIA 4YQSA 3ILKA 3BBHA 5CO4A 4YQ1A 4YQ0A 4YPWA 4YQ5A 4JALA 4PZKA 1NXZA 2V3JA 4YQPA 1V2XA 4J3CA 3OIIA 4YVJA 1J85A 4YQ4A 4RG1A 5GMCA 4YQJA 4L69A 4YQNA 4YQ6A 1GZ0A 3IEFA 1UAMA 3IC6A 2Z0YA 3NK6A 3QUVA 3DCMX 4YQ3A 3GYQA 1P9PA 3O7BA 2YY8A 3BBDA 4XBOA 4MCCA 4KGNA 5D9FA 4H3YA 4IG6A 5GMBA 1NS5A 3KY7A 2CX8A 4H3ZA 2V3KA 3N4JA 4YQGA 4MCBA 4CNEA 4YVHA 4YPZA 4YVKA 4E8BA 4YQRA 1TO0A 4CNFA
chains in the Genus database with same CATH superfamily
4YQKA 3BBEA 4JWFA 1VHKA 3N4KA 2EGVA 2O3AA 4X3MA 1K3RA 4YQQA 1UALA 3KTYA 4YQAA 3KNUA 1X7OA 2EGWA 4CNGA 3KW2A 4YPXA 3NK7A 2QWVA 1TROA 1V6ZA 4YQOA 5GM8A 1RCSA 1Z85A 1WRPR 4YQTA 4YQLA 3OIJA 1UAJA 4YPYA 1TRRA 1VH0A 2QMMA 3AI9X 1O6DA 3L8UA 4YQBA 1IPAA 4FAKA 4YQ2A 5FAIA 4X3LA 2HA8A 4JAKA 3AIAA 1UAKA 4YQ7A 4MCDA 4YQIA 4YVIA 3SSXN 1ZT9A 1X7PA 3ONPA 4YQ8A 4YQCA 4KDZA 2I6DA 1CO0A 3OINA 4YVGA 3E5YA 1MI7R 3AXZA 4JWGA 1OY5A 4CNDA 1ZJRA 4YQDA 4YQ9A 1VHYA 1MXIA 2OZ9R 4YQSA 4JWJA 3ILKA 3BBHA 5CO4A 3G1CA 4YQ1A 4YQ0A 1WRSR 2XDIA 3SSWN 4YPWA 4YQ5A 3WRPA 1JHGA 4JALA 4PZKA 3KORA 3FRWA 1NXZA 2V3JA 4YQPA 1V2XA 4J3CA 3OIIA 4YVJA 1J85A 4YQ4A 4RG1A 5GMCA 4YQJA 4L69A 4YQNA 4YQ6A 1GZ0A 3IEFA 1UAMA 3IC6A 2Z0YA 3NK6A 3QUVA 3DCMX 4YQ3A 3GYQA 1P9PA 3O7BA 2YY8A 3BBDA 4XBOA 4MCCA 4KGNA 5D9FA 4H3YA 4IG6A 5GMBA 1NS5A 3KY7A 4FMWA 2CX8A 4H3ZA 1WRTR 2V3KA 3N4JA 4YQGA 4MCBA 4CNEA 4JWHA 4YVHA 4YPZA 4YVKA 4E8BA 4YQRA 1TO0A 4CNFA
chains in the Genus database with same CATH topology
4YQKA 3BBEA 4JWFA 1VHKA 3N4KA 2EGVA 2O3AA 4X3MA 1K3RA 4YQQA 1UALA 3KTYA 4YQAA 3KNUA 1X7OA 2EGWA 4CNGA 3KW2A 4YPXA 3NK7A 2QWVA 1V6ZA 4YQOA 5GM8A 1Z85A 4YQTA 4YQLA 3OIJA 1UAJA 4YPYA 1VH0A 2QMMA 3AI9X 1O6DA 3L8UA 4YQBA 1IPAA 4FAKA 4YQ2A 5FAIA 4X3LA 2HA8A 4JAKA 3AIAA 1UAKA 4YQ7A 4MCDA 4YQIA 4YVIA 1X7PA 3ONPA 4YQ8A 4YQCA 4KDZA 2I6DA 3OINA 4YVGA 3E5YA 3AXZA 4JWGA 1OY5A 4CNDA 1ZJRA 4YQDA 1VHYA 4YQ9A 1MXIA 4YQSA 4JWJA 3ILKA 3BBHA 5CO4A 4YQ1A 4YQ0A 4YPWA 4YQ5A 4JALA 4PZKA 1NXZA 2V3JA 4YQPA 1V2XA 4J3CA 3OIIA 4YVJA 1J85A 4YQ4A 4RG1A 5GMCA 4YQJA 4L69A 4YQNA 4YQ6A 1GZ0A 3IEFA 1UAMA 3IC6A 2Z0YA 3NK6A 3QUVA 3DCMX 4YQ3A 3GYQA 1P9PA 3O7BA 2YY8A 3BBDA 4XBOA 4MCCA 4KGNA 5D9FA 4H3YA 4IG6A 5GMBA 1NS5A 3KY7A 4FMWA 2CX8A 4H3ZA 2V3KA 3N4JA 4YQGA 4MCBA 4CNEA 4JWHA 4YVHA 4YPZA 4YVKA 4E8BA 4YQRA 1TO0A 4CNFA
chains in the Genus database with same CATH homology


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