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


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