4YQSA

Crystal structure of trmd, a m1g37 trna methyltransferase with sam-competitive compounds
Total Genus 71
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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
71
Knots found
sequence length
248
structure length
237
Chain Sequence
SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGDGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
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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 71
structure length 237
sequence length 248
other databases KnotProt 2.0: K +31
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 4yqsA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yqsA01
1IPAA 4YQQA 1ZJRA 4YQ6A 2EGWA 1X7PA 4YQ0A 4YQPA 4YQKA 4YVIA 4YQLA 3KTYA 5GM8A 4YQ7A 5GMCA 4IG6A 4YPXA 2QMMA 5D9FA 3AXZA 4YQJA 3KY7A 4YQNA 4JAKA 3AIAA 2O3AA 3AI9X 3QUVA 4YQTA 1V6ZA 3KNUA 3ONPA 2QWVA 1OY5A 1J85A 3L8UA 1UAJA 4KGNA 4YQBA 1VHYA 4PZKA 4YPYA 1GZ0A 3N4JA 2Z0YA 2V3KA 4X3LA 3E5YA 4YQSA 4YQ5A 4YQ2A 2I6DA 4YPZA 4CNEA 1TO0A 1X7OA 4YQOA 4H3YA 4YVKA 4YPWA 3NK7A 4H3ZA 1O6DA 4YQ4A 4X3MA 1V2XA 4YQ1A 4YQRA 2YY8A 1UAMA 1UALA 4MCDA 5CO4A 4YQDA 4YVJA 4MCBA 4KDZA 2V3JA 4YQCA 1K3RA 3BBEA 4CNFA 3BBDA 3OIIA 1VH0A 5FAIA 3GYQA 3N4KA 4XBOA 1P9PA 2EGVA 3OINA 4JALA 3ILKA 4RG1A 5GMBA 3KW2A 4L69A 2CX8A 3IC6A 3O7BA 4YQGA 3DCMX 3NK6A 4YQIA 4YQ3A 4YVGA 3OIJA 4CNDA 1Z85A 4MCCA 4YQ9A 4YVHA 4E8BA 1NS5A 1MXIA 4J3CA 4CNGA 1UAKA 4YQ8A 3BBHA 2HA8A 3IEFA 1NXZA 1VHKA 4FAKA 4YQAA
chains in the Genus database with same CATH superfamily
1IPAA 4YQQA 1ZJRA 4YQ6A 2EGWA 1X7PA 4YQ0A 4YQPA 4YQKA 4YVIA 4FMWA 4YQLA 3KTYA 5GM8A 3KORA 4YQ7A 4JWGA 5GMCA 4IG6A 4YPXA 2QMMA 1WRPR 5D9FA 3AXZA 4YQJA 3SSWN 3KY7A 4YQNA 4JAKA 3AIAA 2O3AA 3AI9X 3QUVA 4YQTA 1V6ZA 3KNUA 2XDIA 1WRSR 3ONPA 2QWVA 1OY5A 1J85A 3L8UA 1UAJA 4KGNA 1RCSA 4YQBA 1VHYA 4PZKA 4YPYA 1GZ0A 3N4JA 2Z0YA 2V3KA 4X3LA 3E5YA 4YQSA 2OZ9R 1TRRA 3FRWA 4YQ5A 4YQ2A 4YPZA 2I6DA 4CNEA 1TROA 1TO0A 1X7OA 4YQOA 4H3YA 4YVKA 4YPWA 4JWFA 3NK7A 4H3ZA 1O6DA 4YQ4A 4X3MA 1MI7R 1V2XA 4YQ1A 4YQRA 2YY8A 1UAMA 1UALA 4MCDA 1CO0A 5CO4A 4YQDA 4YVJA 4MCBA 4KDZA 2V3JA 4YQCA 1K3RA 3BBEA 4CNFA 3BBDA 1ZT9A 3OIIA 1VH0A 5FAIA 3GYQA 3N4KA 4XBOA 4JWHA 1P9PA 2EGVA 3OINA 4JALA 3ILKA 4RG1A 5GMBA 3KW2A 4L69A 2CX8A 3SSXN 3IC6A 3O7BA 4YQGA 3DCMX 3NK6A 4YQIA 4YQ3A 4YVGA 3OIJA 3G1CA 4CNDA 1Z85A 3WRPA 4MCCA 4YQ9A 1WRTR 4YVHA 4E8BA 1NS5A 4JWJA 1MXIA 4J3CA 4CNGA 1UAKA 4YQ8A 3BBHA 2HA8A 3IEFA 1NXZA 1VHKA 4FAKA 4YQAA 1JHGA
chains in the Genus database with same CATH topology
1IPAA 4YQQA 1ZJRA 4YQ6A 2EGWA 1X7PA 4YQ0A 4YQPA 4YQKA 4YVIA 4FMWA 4YQLA 3KTYA 5GM8A 4YQ7A 4JWGA 5GMCA 4IG6A 4YPXA 2QMMA 5D9FA 3AXZA 4YQJA 3KY7A 4YQNA 4JAKA 3AIAA 2O3AA 3AI9X 3QUVA 4YQTA 1V6ZA 3KNUA 3ONPA 2QWVA 1OY5A 1J85A 3L8UA 1UAJA 4KGNA 4YQBA 1VHYA 4PZKA 4YPYA 1GZ0A 3N4JA 2Z0YA 2V3KA 4X3LA 3E5YA 4YQSA 4YQ5A 4YQ2A 2I6DA 4YPZA 4CNEA 1TO0A 1X7OA 4YQOA 4H3YA 4YVKA 4YPWA 4JWFA 3NK7A 4H3ZA 1O6DA 4YQ4A 4X3MA 1V2XA 4YQ1A 4YQRA 2YY8A 1UAMA 1UALA 4MCDA 5CO4A 4YQDA 4YVJA 4MCBA 4KDZA 2V3JA 4YQCA 1K3RA 3BBEA 4CNFA 3BBDA 3OIIA 1VH0A 5FAIA 3GYQA 3N4KA 4XBOA 4JWHA 1P9PA 2EGVA 3OINA 4JALA 3ILKA 4RG1A 5GMBA 3KW2A 4L69A 2CX8A 3IC6A 3O7BA 4YQGA 3DCMX 3NK6A 4YQIA 4YQ3A 4YVGA 3OIJA 4CNDA 1Z85A 4MCCA 4YQ9A 4YVHA 4E8BA 1NS5A 4JWJA 1MXIA 4J3CA 4CNGA 1UAKA 4YQ8A 3BBHA 2HA8A 3IEFA 1NXZA 1VHKA 4FAKA 4YQAA
chains in the Genus database with same CATH homology


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