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


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