4YQ3A

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
253
structure length
242
Chain Sequence
GLVPRGSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGDGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHN
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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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publication title Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
rcsb
molecule tags Transferase/transferase inhibitor
source organism Haemophilus influenzae (strain atcc 51907 / dsm 11121 / kw20 / rd)
molecule keywords tRNA (guanine-N(1)-)-methyltransferase
total genus 69
structure length 242
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 4yq3A02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yq3A01
3IC6A 4YPWA 3AIAA 1ZJRA 4YQ1A 4YQLA 3E5YA 3O7BA 3GYQA 4YQTA 4YQKA 4FAKA 1OY5A 4YQIA 4YPXA 1UALA 2Z0YA 4YQOA 1Z85A 2HA8A 2EGVA 3BBEA 4YQ0A 1NS5A 4J3CA 1IPAA 2YY8A 4CNFA 1J85A 4YQRA 4H3YA 4YQ2A 4YVHA 4KGNA 5D9FA 4PZKA 2O3AA 3OIJA 1MXIA 1UAMA 1VHKA 3ILKA 4XBOA 2EGWA 4YPZA 1UAJA 2QWVA 2QMMA 2V3JA 4YQPA 3AI9X 3BBDA 1UAKA 1X7OA 4YQBA 1X7PA 1P9PA 4YQ4A 3BBHA 4X3LA 2V3KA 3ONPA 1VHYA 4X3MA 4MCDA 3NK7A 3OINA 1VH0A 1NXZA 3OIIA 4YQCA 3AXZA 4YQ5A 4MCCA 3DCMX 4YQSA 1GZ0A 1V6ZA 1K3RA 4YVJA 4MCBA 4JALA 5GMCA 4YQJA 4KDZA 4YQDA 4CNGA 4CNEA 4YQ6A 4YVKA 3IEFA 1V2XA 4YPYA 4L69A 4JAKA 3KY7A 4YVIA 5FAIA 4YQ9A 3KTYA 4H3ZA 3QUVA 4YQGA 4YQ7A 4YQ8A 2CX8A 4YQ3A 5CO4A 4YQNA 4YQQA 5GM8A 5GMBA 4CNDA 1O6DA 4IG6A 3N4JA 3KW2A 3L8UA 2I6DA 3KNUA 4E8BA 1TO0A 4YVGA 3N4KA 4YQAA 4RG1A 3NK6A
chains in the Genus database with same CATH superfamily
3IC6A 3SSXN 4YPWA 1WRPR 3AIAA 1ZJRA 4YQ1A 4YQLA 3E5YA 1ZT9A 2XDIA 3O7BA 3GYQA 4YQTA 4YQKA 4FAKA 1OY5A 4YQIA 4YPXA 1CO0A 1RCSA 1UALA 2Z0YA 4YQOA 1Z85A 2HA8A 2EGVA 3BBEA 4YQ0A 1NS5A 3KORA 4J3CA 1IPAA 2YY8A 4CNFA 1J85A 4YQRA 4JWHA 4H3YA 3SSWN 4YQ2A 4YVHA 4KGNA 3FRWA 2OZ9R 5D9FA 4PZKA 2O3AA 3OIJA 1MXIA 4JWGA 1UAMA 1VHKA 3ILKA 1MI7R 4XBOA 2EGWA 4YPZA 1UAJA 2QWVA 2QMMA 2V3JA 4YQPA 3AI9X 3BBDA 1UAKA 1X7OA 4YQBA 1X7PA 1P9PA 4YQ4A 3BBHA 4X3LA 2V3KA 3ONPA 1VHYA 4X3MA 4MCDA 3NK7A 3OINA 1WRSR 1TROA 1VH0A 1NXZA 3OIIA 4YQCA 3AXZA 4YQ5A 4MCCA 4FMWA 3DCMX 4YQSA 1GZ0A 1V6ZA 1K3RA 4YVJA 4MCBA 1WRTR 4JALA 5GMCA 4YQJA 4JWFA 4KDZA 4YQDA 4CNGA 4CNEA 4YQ6A 4YVKA 3IEFA 1V2XA 4YPYA 4L69A 4JAKA 3KY7A 4JWJA 4YVIA 5FAIA 4YQ9A 3KTYA 3G1CA 4H3ZA 3QUVA 1JHGA 4YQGA 4YQ7A 4YQ8A 2CX8A 4YQ3A 5CO4A 3WRPA 4YQNA 4YQQA 5GM8A 5GMBA 4CNDA 1O6DA 4IG6A 3N4JA 3KW2A 3L8UA 2I6DA 3KNUA 4E8BA 1TO0A 4YVGA 3N4KA 4YQAA 4RG1A 3NK6A 1TRRA
chains in the Genus database with same CATH topology
3IC6A 4YPWA 3AIAA 1ZJRA 4YQ1A 4YQLA 3E5YA 3O7BA 3GYQA 4YQTA 4YQKA 4FAKA 1OY5A 4YQIA 4YPXA 1UALA 2Z0YA 4YQOA 1Z85A 2HA8A 2EGVA 3BBEA 4YQ0A 1NS5A 4J3CA 1IPAA 2YY8A 4CNFA 1J85A 4YQRA 4JWHA 4H3YA 4YQ2A 4YVHA 4KGNA 5D9FA 4PZKA 2O3AA 3OIJA 1MXIA 4JWGA 1UAMA 1VHKA 3ILKA 4XBOA 2EGWA 4YPZA 1UAJA 2QWVA 2QMMA 2V3JA 4YQPA 3AI9X 3BBDA 1UAKA 1X7OA 4YQBA 1X7PA 1P9PA 4YQ4A 3BBHA 4X3LA 2V3KA 3ONPA 1VHYA 4X3MA 4MCDA 3NK7A 3OINA 1VH0A 1NXZA 3OIIA 4YQCA 3AXZA 4YQ5A 4MCCA 4FMWA 3DCMX 4YQSA 1GZ0A 1V6ZA 1K3RA 4YVJA 4MCBA 4JALA 5GMCA 4YQJA 4JWFA 4KDZA 4YQDA 4CNGA 4CNEA 4YQ6A 4YVKA 3IEFA 1V2XA 4YPYA 4L69A 4JAKA 3KY7A 4JWJA 4YVIA 5FAIA 4YQ9A 3KTYA 4H3ZA 3QUVA 4YQGA 4YQ7A 4YQ8A 2CX8A 4YQ3A 5CO4A 4YQNA 4YQQA 5GM8A 5GMBA 4CNDA 1O6DA 4IG6A 3N4JA 3KW2A 3L8UA 2I6DA 3KNUA 4E8BA 1TO0A 4YVGA 3N4KA 4YQAA 4RG1A 3NK6A
chains in the Genus database with same CATH homology


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