4YPXA

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
249
structure length
239
Chain Sequence
RGSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHN
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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 239
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 4ypxA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4ypxA01
4YQPA 4YQ4A 1OY5A 1V2XA 1TO0A 4YQQA 4YQ3A 1UAMA 5GMBA 4IG6A 1UALA 1K3RA 2O3AA 4PZKA 4YQ5A 3ONPA 4YQ9A 4YQ7A 3N4JA 1J85A 1O6DA 4JALA 1P9PA 2EGWA 2Z0YA 4X3LA 4L69A 4RG1A 4YQNA 2V3KA 3L8UA 4XBOA 3KW2A 4YVIA 4YQLA 1UAKA 2CX8A 3NK6A 4H3ZA 1UAJA 2YY8A 3OINA 3N4KA 4YQRA 4YQ8A 1GZ0A 3KY7A 3GYQA 3AXZA 4YPXA 2V3JA 3BBHA 3E5YA 5D9FA 1X7PA 4MCBA 5GM8A 1VHKA 4J3CA 1IPAA 4MCCA 1V6ZA 1NS5A 4YVHA 4YPYA 4YQTA 4YQ6A 5GMCA 2HA8A 4YVKA 4H3YA 4YQAA 1Z85A 4YQSA 3KTYA 3BBDA 4X3MA 1MXIA 3DCMX 1VHYA 5FAIA 1VH0A 4YQBA 4YQJA 4CNEA 4YPWA 3ILKA 4YQ1A 4YVGA 4YQGA 2QMMA 3BBEA 4MCDA 2QWVA 3IEFA 4YVJA 4YPZA 3OIJA 4YQ2A 4FAKA 3OIIA 3QUVA 4YQIA 2I6DA 2EGVA 4CNGA 5CO4A 3KNUA 3IC6A 3O7BA 4YQOA 3AI9X 1NXZA 3AIAA 4YQKA 4CNFA 4KGNA 4KDZA 3NK7A 4CNDA 4YQDA 4YQCA 1ZJRA 4YQ0A 4E8BA 4JAKA 1X7OA
chains in the Genus database with same CATH superfamily
3KORA 4YQPA 4YQ4A 1OY5A 1V2XA 1TO0A 4YQQA 4YQ3A 1UAMA 5GMBA 4IG6A 1UALA 1K3RA 2O3AA 4PZKA 4YQ5A 3ONPA 1JHGA 4YQ9A 4YQ7A 3N4JA 1J85A 1O6DA 4JALA 1P9PA 2EGWA 3SSXN 2Z0YA 1WRTR 4X3LA 1RCSA 4L69A 4RG1A 4YQNA 2V3KA 3L8UA 4XBOA 3KW2A 4YQLA 1X7OA 1UAKA 2CX8A 3NK6A 4H3ZA 1UAJA 2YY8A 3OINA 3N4KA 4YQRA 4JWHA 1WRSR 4YQ8A 1GZ0A 3KY7A 3GYQA 3AXZA 4YPXA 2V3JA 3BBHA 3E5YA 5D9FA 1X7PA 4MCBA 5GM8A 1VHKA 4J3CA 1IPAA 4MCCA 1V6ZA 1NS5A 4YVHA 4YPYA 4YQTA 4YQ6A 5GMCA 2HA8A 4YVKA 4H3YA 4YQAA 1CO0A 1Z85A 4YQSA 3KTYA 3BBDA 4X3MA 1MXIA 4JWFA 1MI7R 2XDIA 3DCMX 1VHYA 4FMWA 5FAIA 1TROA 1VH0A 1ZT9A 4YQBA 4YQJA 4CNEA 4YPWA 3ILKA 4YQ1A 4YVGA 4YQGA 2QMMA 3BBEA 3FRWA 4MCDA 4JWJA 3G1CA 3WRPA 2QWVA 3IEFA 1WRPR 2OZ9R 4YVJA 4YPZA 3OIJA 4YQ2A 4FAKA 3OIIA 3QUVA 4YQIA 2I6DA 2EGVA 4CNGA 5CO4A 3KNUA 3IC6A 4JWGA 3O7BA 4YQOA 3AI9X 1NXZA 3AIAA 4YQKA 4CNFA 4KGNA 4KDZA 3NK7A 1TRRA 4CNDA 4YQDA 4YQCA 3SSWN 1ZJRA 4YQ0A 4E8BA 4JAKA 4YVIA
chains in the Genus database with same CATH topology
4YQPA 4YQ4A 1OY5A 1V2XA 1TO0A 4YQQA 4YQ3A 1UAMA 5GMBA 4IG6A 1UALA 1K3RA 2O3AA 4PZKA 4YQ5A 3ONPA 4YQ9A 4YQ7A 3N4JA 1J85A 1O6DA 4JALA 1P9PA 2EGWA 2Z0YA 4X3LA 4L69A 4RG1A 4YQNA 2V3KA 3L8UA 4XBOA 3KW2A 4YVIA 4YQLA 1UAKA 2CX8A 3NK6A 4H3ZA 1UAJA 2YY8A 3OINA 3N4KA 4YQRA 4JWHA 4YQ8A 1GZ0A 3KY7A 3GYQA 3AXZA 4YPXA 2V3JA 3BBHA 3E5YA 5D9FA 1X7PA 4MCBA 5GM8A 1VHKA 4J3CA 1IPAA 4MCCA 1V6ZA 1NS5A 4YVHA 4YPYA 4YQTA 4YQ6A 5GMCA 2HA8A 4YVKA 4H3YA 4YQAA 1Z85A 4YQSA 3KTYA 3BBDA 4X3MA 1MXIA 4JWFA 3DCMX 1VHYA 4FMWA 5FAIA 1VH0A 4YQBA 4YQJA 4CNEA 4YPWA 3ILKA 4YQ1A 4YVGA 4YQGA 2QMMA 3BBEA 4MCDA 4JWJA 2QWVA 3IEFA 4YVJA 4YPZA 3OIJA 4YQ2A 4FAKA 3OIIA 3QUVA 4YQIA 2I6DA 2EGVA 4CNGA 5CO4A 3KNUA 3IC6A 4JWGA 3O7BA 4YQOA 3AI9X 1NXZA 3AIAA 4YQKA 4CNFA 4KGNA 4KDZA 3NK7A 4CNDA 4YQDA 4YQCA 1ZJRA 4YQ0A 4E8BA 4JAKA 1X7OA
chains in the Genus database with same CATH homology


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