4YQRA

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
Knots found
sequence length
248
structure length
240
Chain Sequence
b'SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS'
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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 keywords tRNA (guanine-N(1)-)-methyltransferase
source organism Haemophilus influenzae (strain atcc 51907 / dsm 11121 / kw20 / rd)
molecule tags Transferase/transferase inhibitor
total genus 74
structure length 240
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 4yqrA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yqrA01
4YVIA 4RG1A 5GMCA 1VHKA 4YQPA 4YPZA 3N4KA 3AXZA 4YQGA 1P9PA 4YQTA 4YQNA 2CX8A 3L8UA 2O3AA 3ILKA 3E5YA 3DCMX 5CO4A 4E8BA 3KY7A 1X7PA 4YQAA 4H3YA 4CNFA 4YQKA 3OINA 1X7OA 4YPXA 4L69A 5GM8A 1UAJA 4CNGA 4YQDA 3N4JA 4FAKA 4YQLA 2V3KA 4YQOA 4YVKA 1TO0A 3QUVA 4CNDA 3NK7A 4PZKA 3KNUA 3KTYA 4YQ5A 1UAKA 4YQCA 4YQ2A 3BBDA 4CNEA 3OIJA 1V2XA 4KGNA 4YQRA 1ZJRA 4YQ4A 1VH0A 3IC6A 1MXIA 4X3MA 4YQBA 4MCBA 4YQ7A 4YVHA 1NS5A 3OIIA 4YQ9A 2Z0YA 3BBEA 4YPYA 4IG6A 4YQ0A 4YQIA 3AIAA 1IPAA 1UALA 1V6ZA 2HA8A 5FAIA 3NK6A 4YQ3A 5D9FA 4MCDA 4JALA 3BBHA 5GMBA 4YQ1A 1O6DA 4XBOA 1J85A 3O7BA 1NXZA 1GZ0A 4X3LA 2QWVA 4YVGA 2EGWA 4J3CA 1Z85A 4YQJA 4YQQA 2YY8A 4YQ6A 4MCCA 4YQSA 3ONPA 2V3JA 4JAKA 4YPWA 2EGVA 1UAMA 4YVJA 4KDZA 4H3ZA 2I6DA 1OY5A 2QMMA 3AI9X 3GYQA 1VHYA 1K3RA 4YQ8A 3KW2A 3IEFA
chains in the Genus database with same CATH superfamily
4YVIA 4RG1A 5GMCA 1VHKA 2OZ9R 4YQPA 4YPZA 3N4KA 3AXZA 4YQGA 1P9PA 3FRWA 4YQTA 4YQNA 1WRPR 4JWJA 2CX8A 3L8UA 2O3AA 3ILKA 3E5YA 3DCMX 5CO4A 4E8BA 3KY7A 1X7PA 4YQAA 4H3YA 4CNFA 4YQKA 3SSWN 3OINA 4YPXA 1X7OA 4L69A 5GM8A 1UAJA 4CNGA 4YQDA 3N4JA 4FAKA 1WRSR 4YQLA 1RCSA 2V3KA 2XDIA 4YQOA 4YVKA 1TO0A 3QUVA 4CNDA 3NK7A 4PZKA 3KNUA 3KTYA 4JWFA 4YQ5A 1UAKA 4YQCA 4YQ2A 3BBDA 4FMWA 4CNEA 3OIJA 1V2XA 4KGNA 4YQRA 1ZJRA 1CO0A 4YQ4A 1VH0A 3IC6A 1MXIA 4X3MA 3WRPA 4YQBA 4MCBA 4YQ7A 4YVHA 1NS5A 1WRTR 3OIIA 4YQ9A 2Z0YA 3BBEA 4JWGA 4YPYA 4IG6A 4YQ0A 4YQIA 3AIAA 1JHGA 1IPAA 1UALA 1V6ZA 2HA8A 5FAIA 3NK6A 4YQ3A 1TRRA 5D9FA 4MCDA 4JALA 3BBHA 5GMBA 4YQ1A 1O6DA 4JWHA 4XBOA 1J85A 3O7BA 1NXZA 1GZ0A 4X3LA 2QWVA 4YVGA 3KORA 2EGWA 1MI7R 4J3CA 3G1CA 1Z85A 4YQJA 4YQQA 2YY8A 4YQ6A 4MCCA 4YQSA 3ONPA 2V3JA 4JAKA 4YPWA 1ZT9A 2EGVA 1UAMA 4YVJA 4KDZA 4H3ZA 2I6DA 1OY5A 3SSXN 2QMMA 3AI9X 3GYQA 1TROA 1VHYA 1K3RA 4YQ8A 3KW2A 3IEFA
chains in the Genus database with same CATH topology
4YVIA 4RG1A 5GMCA 1VHKA 4YQPA 4YPZA 3N4KA 3AXZA 4YQGA 1P9PA 4YQTA 4YQNA 4JWJA 2CX8A 3L8UA 2O3AA 3ILKA 3E5YA 3DCMX 5CO4A 4E8BA 3KY7A 1X7PA 4YQAA 4H3YA 4CNFA 4YQKA 3OINA 1X7OA 4YPXA 4L69A 5GM8A 1UAJA 4CNGA 4YQDA 3N4JA 4FAKA 4YQLA 2V3KA 4YQOA 4YVKA 1TO0A 3QUVA 4CNDA 3NK7A 4PZKA 3KNUA 3KTYA 4JWFA 4YQ5A 1UAKA 4YQCA 4YQ2A 3BBDA 4FMWA 4CNEA 3OIJA 1V2XA 4KGNA 4YQRA 1ZJRA 4YQ4A 1VH0A 3IC6A 1MXIA 4X3MA 4YQBA 4MCBA 4YQ7A 4YVHA 1NS5A 3OIIA 4YQ9A 2Z0YA 3BBEA 4JWGA 4YPYA 4IG6A 4YQ0A 4YQIA 3AIAA 1IPAA 1UALA 1V6ZA 2HA8A 5FAIA 3NK6A 4YQ3A 5D9FA 4MCDA 4JALA 3BBHA 5GMBA 4YQ1A 1O6DA 4JWHA 4XBOA 1J85A 3O7BA 1NXZA 1GZ0A 4X3LA 2QWVA 4YVGA 2EGWA 4J3CA 1Z85A 4YQJA 4YQQA 2YY8A 4YQ6A 4MCCA 4YQSA 3ONPA 2V3JA 4JAKA 4YPWA 2EGVA 1UAMA 4YVJA 4KDZA 4H3ZA 2I6DA 1OY5A 2QMMA 3AI9X 3GYQA 1VHYA 1K3RA 4YQ8A 3KW2A 3IEFA
chains in the Genus database with same CATH homology


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