4YQTA

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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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 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 4yqtA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yqtA01
4YVHA 4YQRA 4YQ8A 2CX8A 3E5YA 4YQDA 4YQ4A 2I6DA 2Z0YA 3QUVA 4YQ7A 1O6DA 3AIAA 4X3LA 3AXZA 4CNGA 1K3RA 3IEFA 4IG6A 2QMMA 3KY7A 4MCBA 4XBOA 4YQKA 4CNEA 4KDZA 2EGVA 1UAKA 4H3YA 4YQJA 3KNUA 4YQSA 4YQPA 4YPZA 4YQIA 4YQTA 5GMCA 4YVJA 4YVIA 3N4KA 3NK6A 1X7OA 4YQBA 4YQGA 1J85A 4YPYA 4YQ5A 1V6ZA 3ONPA 4JALA 5GM8A 1UAJA 4JAKA 4CNFA 1VHYA 4J3CA 2V3JA 1VHKA 3OIIA 1VH0A 4YVGA 4YQNA 3ILKA 4PZKA 4MCCA 4YQAA 4YQ0A 3NK7A 3KW2A 4L69A 3DCMX 1ZJRA 5CO4A 1Z85A 2QWVA 1UAMA 4YPXA 4FAKA 1OY5A 2EGWA 4YQCA 4YQ9A 1MXIA 3BBDA 2O3AA 3BBHA 3O7BA 1IPAA 1UALA 4E8BA 1X7PA 4YQ6A 4CNDA 4YQ1A 2YY8A 5FAIA 4H3ZA 4YQ3A 5D9FA 3AI9X 1NXZA 4MCDA 2HA8A 4RG1A 4YPWA 3KTYA 4YQLA 4YQOA 3N4JA 3OINA 4YVKA 1P9PA 1V2XA 4X3MA 4YQQA 1GZ0A 3L8UA 4YQ2A 3GYQA 2V3KA 4KGNA 1TO0A 1NS5A 3OIJA 5GMBA 3IC6A 3BBEA
chains in the Genus database with same CATH superfamily
4YVHA 4YQRA 4YQ8A 2CX8A 3E5YA 4YQDA 1RCSA 4YQ4A 3FRWA 1CO0A 2I6DA 2Z0YA 3QUVA 4YQ7A 1O6DA 3AIAA 4X3LA 3AXZA 4CNGA 1K3RA 3IEFA 4IG6A 2XDIA 2QMMA 3KY7A 4MCBA 4XBOA 4YQKA 4CNEA 4KDZA 2EGVA 1UAKA 4H3YA 4YQJA 3KNUA 4YQSA 1MI7R 4YQPA 1WRTR 4YPZA 4YQIA 4YQTA 5GMCA 3KORA 4YVJA 4YVIA 3N4KA 3NK6A 1X7OA 4YQBA 4YQGA 1J85A 4JWFA 4JWGA 4YPYA 4YQ5A 3SSWN 1V6ZA 3ONPA 3WRPA 4JALA 5GM8A 1UAJA 4JAKA 4CNFA 1VHYA 4J3CA 2V3JA 1VHKA 3OIIA 4YVGA 1VH0A 4JWJA 4YQNA 3ILKA 4PZKA 4MCCA 4YQAA 4YQ0A 3NK7A 3KW2A 4L69A 2OZ9R 3DCMX 1ZJRA 1TRRA 5CO4A 1WRPR 4FMWA 1Z85A 2QWVA 1UAMA 4YPXA 4FAKA 3G1CA 1OY5A 2EGWA 4YQCA 1WRSR 4YQ9A 1MXIA 3BBDA 2O3AA 3BBHA 3O7BA 1IPAA 1UALA 4E8BA 1X7PA 4YQ6A 4CNDA 1JHGA 4YQ1A 3SSXN 2YY8A 5FAIA 4H3ZA 4YQ3A 5D9FA 3AI9X 1NXZA 4MCDA 2HA8A 4RG1A 4YPWA 3KTYA 1ZT9A 4YQLA 4JWHA 4YQOA 3N4JA 3OINA 4YVKA 1P9PA 1V2XA 4X3MA 4YQQA 1GZ0A 1TROA 3L8UA 4YQ2A 3GYQA 2V3KA 4KGNA 1TO0A 1NS5A 3OIJA 5GMBA 3IC6A 3BBEA
chains in the Genus database with same CATH topology
4YVHA 4YQRA 4YQ8A 2CX8A 3E5YA 4YQDA 4YQ4A 2I6DA 2Z0YA 3QUVA 4YQ7A 1O6DA 3AIAA 4X3LA 3AXZA 4CNGA 1K3RA 3IEFA 4IG6A 2QMMA 3KY7A 4MCBA 4XBOA 4YQKA 4CNEA 4KDZA 2EGVA 1UAKA 4H3YA 4YQJA 3KNUA 4YQSA 4YQPA 4YPZA 4YQIA 4YQTA 5GMCA 4YVJA 4YVIA 3N4KA 3NK6A 1X7OA 4YQBA 4YQGA 1J85A 4JWFA 4JWGA 4YPYA 4YQ5A 1V6ZA 3ONPA 4JALA 5GM8A 1UAJA 4JAKA 4CNFA 1VHYA 4J3CA 2V3JA 1VHKA 3OIIA 1VH0A 4YVGA 4JWJA 4YQNA 3ILKA 4PZKA 4MCCA 4YQAA 4YQ0A 3NK7A 3KW2A 4L69A 3DCMX 1ZJRA 5CO4A 4FMWA 1Z85A 2QWVA 1UAMA 4YPXA 4FAKA 1OY5A 2EGWA 4YQCA 4YQ9A 1MXIA 3BBDA 2O3AA 3BBHA 3O7BA 1IPAA 1UALA 4E8BA 1X7PA 4YQ6A 4CNDA 4YQ1A 2YY8A 5FAIA 4H3ZA 4YQ3A 5D9FA 3AI9X 1NXZA 4MCDA 2HA8A 4RG1A 4YPWA 3KTYA 4YQLA 4JWHA 4YQOA 3N4JA 3OINA 4YVKA 1P9PA 1V2XA 4X3MA 4YQQA 1GZ0A 3L8UA 4YQ2A 3GYQA 2V3KA 4KGNA 1TO0A 1NS5A 3OIJA 5GMBA 3IC6A 3BBEA
chains in the Genus database with same CATH homology


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