4YQSA

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 4yqsA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yqsA01
4IG6A 4YQPA 3OINA 4CNEA 1VHYA 1K3RA 4YQDA 4KGNA 1V2XA 1UALA 3E5YA 1ZJRA 4YQQA 3NK7A 3N4KA 3AI9X 1UAMA 2V3KA 4L69A 4YPWA 4YQ7A 1GZ0A 1UAKA 4YQ2A 4MCDA 4YVJA 4JALA 3OIIA 4YQSA 1VHKA 1TO0A 3GYQA 3ILKA 3BBDA 3KY7A 1NS5A 4YQ4A 4YQCA 3O7BA 4YQ8A 2CX8A 1OY5A 4YQ6A 3L8UA 5GMCA 3KNUA 4YQOA 1O6DA 4YQ3A 1MXIA 4MCBA 1Z85A 1J85A 3BBEA 4H3YA 4FAKA 4YQLA 3KTYA 3N4JA 4YPYA 1V6ZA 4YQBA 4X3LA 4E8BA 4YQGA 4YQIA 5D9FA 4YPZA 4JAKA 1X7OA 4RG1A 2HA8A 1P9PA 4YQTA 4CNFA 5GM8A 4YQ1A 4X3MA 4YVHA 4PZKA 1VH0A 1UAJA 4YPXA 3NK6A 2Z0YA 5CO4A 4YQAA 4YQ9A 3DCMX 1IPAA 3BBHA 3ONPA 4CNGA 4YQKA 3IC6A 4YQJA 3OIJA 4YQ5A 5GMBA 4CNDA 3AIAA 4KDZA 3KW2A 4YQRA 5FAIA 1NXZA 2I6DA 4YVGA 4YQNA 4J3CA 3IEFA 4MCCA 2QMMA 4YVKA 2YY8A 4YQ0A 3AXZA 4H3ZA 3QUVA 2EGWA 2V3JA 4YVIA 4XBOA 1X7PA 2QWVA 2O3AA 2EGVA
chains in the Genus database with same CATH superfamily
4IG6A 4YQPA 3OINA 1JHGA 4CNEA 1VHYA 1K3RA 4YQDA 4KGNA 1V2XA 1UALA 3E5YA 1ZJRA 4YQQA 3NK7A 3N4KA 3AI9X 1UAMA 3G1CA 2V3KA 4L69A 4YPWA 4YQ7A 1CO0A 1GZ0A 1TROA 1UAKA 4YQ2A 4MCDA 4YVJA 4JALA 3OIIA 4YQSA 1VHKA 1TO0A 3GYQA 3ILKA 3BBDA 3KY7A 1NS5A 4YQ4A 4YQCA 3O7BA 4YQ8A 2CX8A 1OY5A 4YQ6A 2XDIA 3L8UA 5GMCA 3KNUA 4YQOA 1O6DA 4YQ3A 1ZT9A 1MXIA 4MCBA 1Z85A 4JWGA 1WRTR 1WRSR 1J85A 3BBEA 4H3YA 4FAKA 4YQLA 3KTYA 4JWHA 3N4JA 4YPYA 1V6ZA 4YQBA 4X3LA 4E8BA 4YQGA 4YQIA 5D9FA 4YPZA 4JAKA 1X7OA 4RG1A 2HA8A 1P9PA 4YQTA 3SSWN 2OZ9R 4CNFA 5GM8A 3FRWA 4YQ1A 4X3MA 4YVHA 1TRRA 4PZKA 1VH0A 1UAJA 4YPXA 4FMWA 3NK6A 2Z0YA 5CO4A 1MI7R 1RCSA 4YQAA 4YQ9A 3DCMX 1IPAA 3BBHA 3ONPA 4JWFA 3SSXN 4CNGA 4YQKA 3IC6A 4YQJA 3OIJA 4YQ5A 5GMBA 3WRPA 4CNDA 3AIAA 4KDZA 3KW2A 4YQRA 5FAIA 1NXZA 2I6DA 1WRPR 4YVGA 4YQNA 4J3CA 4JWJA 3IEFA 4MCCA 2QMMA 4YVKA 2YY8A 4YQ0A 3AXZA 4H3ZA 3KORA 3QUVA 2EGWA 2V3JA 4YVIA 4XBOA 1X7PA 2QWVA 2O3AA 2EGVA
chains in the Genus database with same CATH topology
4IG6A 4YQPA 3OINA 4CNEA 1VHYA 1K3RA 4YQDA 4KGNA 1V2XA 1UALA 3E5YA 1ZJRA 4YQQA 3NK7A 3N4KA 3AI9X 1UAMA 2V3KA 4L69A 4YPWA 4YQ7A 1GZ0A 1UAKA 4YQ2A 4MCDA 4YVJA 4JALA 3OIIA 4YQSA 1VHKA 1TO0A 3GYQA 3ILKA 3BBDA 3KY7A 1NS5A 4YQ4A 4YQCA 3O7BA 4YQ8A 2CX8A 1OY5A 4YQ6A 3L8UA 5GMCA 3KNUA 4YQOA 1O6DA 4YQ3A 1MXIA 4MCBA 1Z85A 4JWGA 1J85A 3BBEA 4H3YA 4FAKA 4YQLA 3KTYA 4JWHA 3N4JA 4YPYA 1V6ZA 4YQBA 4X3LA 4E8BA 4YQGA 4YQIA 5D9FA 4YPZA 4JAKA 1X7OA 4RG1A 2HA8A 1P9PA 4YQTA 4CNFA 5GM8A 4YQ1A 4X3MA 4YVHA 4PZKA 1VH0A 1UAJA 4YPXA 4FMWA 3NK6A 2Z0YA 5CO4A 4YQAA 4YQ9A 3DCMX 1IPAA 3BBHA 3ONPA 4JWFA 4CNGA 4YQKA 3IC6A 4YQJA 3OIJA 4YQ5A 5GMBA 4CNDA 3AIAA 4KDZA 3KW2A 4YQRA 5FAIA 1NXZA 2I6DA 4YVGA 4YQNA 4J3CA 4JWJA 3IEFA 4MCCA 2QMMA 4YVKA 2YY8A 4YQ0A 3AXZA 4H3ZA 3QUVA 2EGWA 2V3JA 4YVIA 4XBOA 1X7PA 2QWVA 2O3AA 2EGVA
chains in the Genus database with same CATH homology


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