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


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