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


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