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


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