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


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