4YQRA

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
248
structure length
240
Chain Sequence
SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
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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 74
structure length 240
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 4yqrA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yqrA01
4MCDA 1O6DA 3N4JA 3AI9X 4YQRA 4H3YA 4YQIA 4YVIA 2EGWA 4KGNA 4YQLA 4CNDA 4MCBA 4YQ2A 4FAKA 3GYQA 1NXZA 3OINA 1X7PA 1P9PA 2HA8A 3L8UA 3O7BA 3BBHA 4YVKA 3IC6A 3IEFA 2I6DA 4X3LA 4JAKA 5GMBA 1NS5A 1VHKA 3NK6A 1ZJRA 3ONPA 1K3RA 4YVJA 4YQKA 4YQ7A 4YPWA 4YQ5A 4YVGA 3NK7A 4PZKA 4YQTA 2V3KA 1UAKA 4RG1A 4YQ0A 4YPZA 3BBEA 2QWVA 4YVHA 1MXIA 2V3JA 1X7OA 3KNUA 2Z0YA 4CNGA 4YQ1A 5GMCA 1VH0A 4YQQA 3AIAA 4YQCA 4YPYA 1TO0A 4MCCA 4YQPA 4YQ9A 1Z85A 4YQOA 3KTYA 4KDZA 3OIIA 1V2XA 3DCMX 5D9FA 3ILKA 3OIJA 4H3ZA 3AXZA 3E5YA 3N4KA 4YQSA 3KY7A 4YQJA 2QMMA 1IPAA 2CX8A 4CNFA 4YQAA 4YQ6A 4YPXA 4L69A 2YY8A 4YQGA 1OY5A 3QUVA 4J3CA 4YQ8A 4YQDA 4YQBA 4XBOA 1V6ZA 5GM8A 4JALA 1UALA 3KW2A 5CO4A 4IG6A 4YQ3A 4YQ4A 4X3MA 2O3AA 4E8BA 1VHYA 1UAJA 1GZ0A 4CNEA 1UAMA 1J85A 4YQNA 3BBDA 5FAIA 2EGVA
chains in the Genus database with same CATH superfamily
4MCDA 1O6DA 3N4JA 3AI9X 1TRRA 4YQRA 4H3YA 4YQIA 4YVIA 2EGWA 4KGNA 4YQLA 4CNDA 1RCSA 4YQ2A 4MCBA 1WRSR 4FAKA 3GYQA 3SSXN 1NXZA 3OINA 1X7PA 1CO0A 1P9PA 4JWHA 2HA8A 3L8UA 3O7BA 3BBHA 4YVKA 1TROA 3IC6A 3IEFA 2I6DA 4X3LA 4JAKA 5GMBA 1NS5A 1VHKA 3NK6A 3KORA 1ZJRA 3ONPA 1ZT9A 4YVJA 1K3RA 4YQKA 4YQ7A 4YPWA 4YQ5A 4YVGA 3NK7A 4PZKA 4YQTA 2V3KA 1UAKA 1WRPR 4RG1A 3WRPA 4YQ0A 4YPZA 3FRWA 3BBEA 2QWVA 4YVHA 4FMWA 1MXIA 2V3JA 1X7OA 3KNUA 2Z0YA 4JWGA 4CNGA 4YQ1A 2OZ9R 5GMCA 3G1CA 1VH0A 4YQQA 3AIAA 4YQCA 4YPYA 1TO0A 4MCCA 4YQPA 4YQ9A 1Z85A 4YQOA 3KTYA 4KDZA 3OIIA 1V2XA 4JWFA 3DCMX 5D9FA 3ILKA 2XDIA 4H3ZA 3OIJA 3AXZA 3E5YA 3N4KA 4YQSA 3KY7A 4YQJA 2QMMA 1JHGA 1IPAA 1WRTR 2CX8A 4JWJA 4CNFA 4YQAA 4YQ6A 4YPXA 4L69A 2YY8A 4YQGA 1OY5A 3QUVA 4J3CA 4YQ8A 4YQDA 4YQBA 4XBOA 1MI7R 1V6ZA 5GM8A 4JALA 1UALA 3KW2A 5CO4A 4IG6A 4YQ3A 4YQ4A 3SSWN 4X3MA 2O3AA 4E8BA 1VHYA 1UAJA 1GZ0A 4CNEA 1UAMA 1J85A 4YQNA 3BBDA 5FAIA 2EGVA
chains in the Genus database with same CATH topology
4MCDA 1O6DA 3N4JA 3AI9X 4YQRA 4H3YA 4YQIA 4YVIA 2EGWA 4KGNA 4YQLA 4CNDA 4MCBA 4YQ2A 4FAKA 3GYQA 1NXZA 3OINA 1X7PA 1P9PA 4JWHA 2HA8A 3L8UA 3O7BA 3BBHA 4YVKA 3IC6A 3IEFA 2I6DA 4X3LA 4JAKA 5GMBA 1NS5A 1VHKA 3NK6A 1ZJRA 3ONPA 1K3RA 4YVJA 4YQKA 4YQ7A 4YPWA 4YQ5A 4YVGA 3NK7A 4PZKA 4YQTA 2V3KA 1UAKA 4RG1A 4YQ0A 4YPZA 3BBEA 2QWVA 4YVHA 4FMWA 1MXIA 2V3JA 1X7OA 3KNUA 2Z0YA 4JWGA 4CNGA 4YQ1A 5GMCA 1VH0A 4YQQA 3AIAA 4YQCA 4YPYA 1TO0A 4MCCA 4YQPA 4YQ9A 1Z85A 4YQOA 3KTYA 4KDZA 3OIIA 1V2XA 4JWFA 3DCMX 5D9FA 3ILKA 3OIJA 4H3ZA 3AXZA 3E5YA 3N4KA 4YQSA 3KY7A 4YQJA 2QMMA 1IPAA 2CX8A 4JWJA 4CNFA 4YQAA 4YQ6A 4YPXA 4L69A 2YY8A 4YQGA 1OY5A 3QUVA 4J3CA 4YQ8A 4YQDA 4YQBA 4XBOA 1V6ZA 5GM8A 4JALA 1UALA 3KW2A 5CO4A 4IG6A 4YQ3A 4YQ4A 4X3MA 2O3AA 4E8BA 1VHYA 1UAJA 1GZ0A 4CNEA 1UAMA 1J85A 4YQNA 3BBDA 5FAIA 2EGVA
chains in the Genus database with same CATH homology


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