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


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