4YQDA

Crystal structure of trmd, a m1g37 trna methyltransferase with sam-competitive compounds
Total Genus 70
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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
70
Knots found
sequence length
249
structure length
244
Chain Sequence
GSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGASASFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
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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 70
structure length 244
sequence length 249
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 4yqdA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yqdA01
4YPYA 2CX8A 4IG6A 2YY8A 2Z0YA 1O6DA 4YQ4A 1VH0A 4YQAA 4YQLA 4CNGA 4CNEA 4CNFA 4H3ZA 2I6DA 4MCDA 3DCMX 4YQQA 1NS5A 3ILKA 4YQIA 4KDZA 3OINA 4YQBA 4JAKA 4E8BA 4XBOA 2QWVA 1GZ0A 3KNUA 4YQ2A 4YQ9A 5GMBA 4YPWA 2QMMA 3IC6A 3KTYA 3KW2A 2HA8A 1X7PA 1OY5A 4YVGA 2EGWA 4YQTA 2V3JA 3QUVA 4RG1A 4JALA 4YVKA 3N4KA 4YQ1A 1V6ZA 4YQOA 4YPZA 1J85A 4YVHA 4YQ0A 5GM8A 3GYQA 4YQKA 3BBHA 3NK7A 3O7BA 1VHKA 3L8UA 3BBDA 4YQNA 4X3LA 1ZJRA 4MCCA 3AI9X 4H3YA 4YQSA 5CO4A 1Z85A 3ONPA 1NXZA 1UAJA 1TO0A 4MCBA 3NK6A 4YQRA 4YQCA 4CNDA 3KY7A 4YQ6A 4FAKA 1X7OA 3OIJA 4YQPA 4X3MA 5FAIA 2EGVA 1MXIA 1VHYA 4YQ3A 3AXZA 4YVIA 5D9FA 4YQ5A 4YPXA 3E5YA 5GMCA 3N4JA 2O3AA 4YQJA 1UAMA 1UAKA 4YVJA 1K3RA 4YQ7A 3IEFA 4YQGA 4KGNA 1IPAA 3AIAA 3OIIA 4J3CA 4PZKA 1UALA 3BBEA 4YQ8A 4YQDA 4L69A 1P9PA 2V3KA 1V2XA
chains in the Genus database with same CATH superfamily
4YPYA 2CX8A 4IG6A 2YY8A 2Z0YA 3G1CA 1O6DA 4YQ4A 1VH0A 4YQAA 4YQLA 4CNGA 4CNEA 4CNFA 4H3ZA 1ZT9A 2I6DA 3WRPA 4MCDA 3DCMX 4YQQA 1NS5A 1JHGA 3ILKA 4YQIA 1TRRA 4KDZA 3OINA 4YQBA 4JAKA 4E8BA 1MI7R 3FRWA 1WRSR 4XBOA 2QWVA 1GZ0A 3KNUA 4YQ2A 4YQ9A 5GMBA 4YPWA 2QMMA 3IC6A 3KTYA 3KW2A 2HA8A 1TROA 4FMWA 1X7PA 1OY5A 4YVGA 2EGWA 4YQTA 2V3JA 3QUVA 3KORA 4RG1A 4JALA 4YVKA 3N4KA 3SSWN 4YQ1A 1CO0A 1V6ZA 4YQOA 4YPZA 1J85A 4YVHA 4YQ0A 5GM8A 3GYQA 4YQKA 3BBHA 3NK7A 3O7BA 1VHKA 3L8UA 3BBDA 4YQNA 4X3LA 1ZJRA 4JWHA 4MCCA 3AI9X 4H3YA 4YQSA 5CO4A 1RCSA 3SSXN 1Z85A 3ONPA 1NXZA 1UAJA 1TO0A 4MCBA 4JWGA 1WRTR 3NK6A 4YQRA 4YQCA 4CNDA 3KY7A 4YQ6A 4FAKA 1X7OA 1WRPR 4JWFA 3OIJA 4YQPA 4X3MA 5FAIA 2EGVA 2XDIA 1MXIA 1VHYA 4YQ3A 3AXZA 4YVIA 5D9FA 4YQ5A 4YPXA 3E5YA 5GMCA 3N4JA 2O3AA 4YQJA 1UAMA 1UAKA 4YVJA 1K3RA 4YQ7A 3IEFA 4YQGA 4KGNA 1IPAA 3AIAA 2OZ9R 3OIIA 4J3CA 4PZKA 1UALA 3BBEA 4YQ8A 4YQDA 4JWJA 4L69A 1P9PA 2V3KA 1V2XA
chains in the Genus database with same CATH topology
4YPYA 2CX8A 4IG6A 2YY8A 2Z0YA 1O6DA 4YQ4A 1VH0A 4YQAA 4YQLA 4CNGA 4CNEA 4CNFA 4H3ZA 2I6DA 4MCDA 3DCMX 4YQQA 1NS5A 3ILKA 4YQIA 4KDZA 3OINA 4YQBA 4JAKA 4E8BA 4XBOA 2QWVA 1GZ0A 3KNUA 4YQ2A 4YQ9A 5GMBA 4YPWA 2QMMA 3IC6A 3KTYA 3KW2A 2HA8A 4FMWA 1X7PA 1OY5A 4YVGA 2EGWA 4YQTA 2V3JA 3QUVA 4RG1A 4JALA 4YVKA 3N4KA 4YQ1A 1V6ZA 4YQOA 4YPZA 1J85A 4YVHA 4YQ0A 5GM8A 3GYQA 4YQKA 3BBHA 3NK7A 3O7BA 1VHKA 3L8UA 3BBDA 4YQNA 4X3LA 1ZJRA 4JWHA 4MCCA 3AI9X 4H3YA 4YQSA 5CO4A 1Z85A 3ONPA 1NXZA 1UAJA 1TO0A 4MCBA 4JWGA 3NK6A 4YQRA 4YQCA 4CNDA 3KY7A 4YQ6A 4FAKA 1X7OA 4JWFA 3OIJA 4YQPA 4X3MA 5FAIA 2EGVA 1MXIA 1VHYA 4YQ3A 3AXZA 4YVIA 5D9FA 4YQ5A 4YPXA 3E5YA 5GMCA 3N4JA 2O3AA 4YQJA 1UAMA 1UAKA 4YVJA 1K3RA 4YQ7A 3IEFA 4YQGA 4KGNA 1IPAA 3AIAA 3OIIA 4J3CA 4PZKA 1UALA 3BBEA 4YQ8A 4YQDA 4JWJA 4L69A 1P9PA 2V3KA 1V2XA
chains in the Genus database with same CATH homology


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