4YVJA

Crystal structure of h. influenzae trmd in complex with sinefungin and trna variant (g36u)
Total Genus 68
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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
68
Knots found
sequence length
248
structure length
239
Chain Sequence
SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
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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 tags Transferase/rna
molecule keywords tRNA (guanine-N(1)-)-methyltransferase
publication title Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
pubmed doi rcsb
source organism Haemophilus influenzae (strain atcc 51907 / dsm 11121 / kw20 / rd)
total genus 68
structure length 239
sequence length 248
chains with identical sequence B
other databases KnotProt 2.0: K +31
ec nomenclature ec 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
pdb deposition date 2015-03-20

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 4yvjA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yvjA01
3KY7A 3L8UA 1UAKA 4YPZA 4YVHA 4YPWA 4YQIA 1VH0A 4YQOA 3BBEA 2V3JA 3E5YA 4E8BA 3OINA 2CX8A 4YQ5A 4YPXA 3ILKA 1UAJA 5D9FA 3KNUA 3OIIA 4YQBA 1J85A 4KDZA 3O7BA 4X3LA 1X7OA 2QMMA 3IEFA 4YQLA 1MXIA 3AIAA 4YQQA 4YVIA 4XBOA 5GMBA 1GZ0A 4YQSA 3KTYA 4CNGA 1VHYA 4YQ9A 4JAKA 4YQ7A 4YQAA 4H3ZA 1ZJRA 4YQNA 4YQGA 3GYQA 4YQ3A 3OIJA 2I6DA 4KGNA 4IG6A 4L69A 4YVKA 2EGWA 4YPYA 4YQKA 1X7PA 1NS5A 3NK6A 3AXZA 4RG1A 4CNFA 4H3YA 4X3MA 3DCMX 4YQPA 4PZKA 3N4KA 1UAMA 4CNEA 4FAKA 4YQ6A 5GMCA 3QUVA 3ONPA 1V2XA 4YQ8A 4YVGA 4YQ2A 4YQDA 5GM8A 3AI9X 4YQ4A 5FAIA 1VHKA 2Z0YA 2V3KA 4YVJA 4YQ0A 1O6DA 2HA8A 1TO0A 3BBHA 1V6ZA 3N4JA 4MCCA 1NXZA 4YQ1A 4YQTA 4YQCA 2EGVA 4J3CA 4YQRA 2QWVA 3BBDA 1K3RA 5CO4A 3KW2A 1P9PA 1UALA 4JALA 1Z85A 1IPAA 3IC6A 1OY5A 4CNDA 3NK7A 4YQJA 2YY8A 4MCBA 2O3AA 4MCDA
chains in the Genus database with same CATH superfamily
3KY7A 3L8UA 1UAKA 4YPZA 3WRPA 4YVHA 4YPWA 4YQIA 1VH0A 4YQOA 3BBEA 2V3JA 3E5YA 3KORA 4E8BA 3OINA 2CX8A 4YQ5A 4YPXA 3ILKA 1UAJA 5D9FA 3KNUA 3OIIA 4YQBA 1J85A 4KDZA 3O7BA 1MI7R 4X3LA 1WRTR 1X7OA 2QMMA 3IEFA 4YQLA 1MXIA 3AIAA 4YQQA 3SSWN 4YVIA 4XBOA 5GMBA 1TROA 1GZ0A 4YQSA 3KTYA 4CNGA 2OZ9R 1VHYA 4YQ9A 4JAKA 4YQ7A 4YQAA 4H3ZA 4FMWA 1ZJRA 4YQNA 4YQGA 2XDIA 3GYQA 4YQ3A 3OIJA 2I6DA 4KGNA 4IG6A 4L69A 4YVKA 2EGWA 4YPYA 4YQKA 1X7PA 1NS5A 3NK6A 3AXZA 4JWFA 4RG1A 4CNFA 4H3YA 4X3MA 3DCMX 4YQPA 4PZKA 1ZT9A 3N4KA 1UAMA 1WRSR 1TRRA 4CNEA 4FAKA 4YQ6A 5GMCA 3QUVA 3ONPA 1V2XA 4YQ8A 4YVGA 4YQ2A 4YQDA 5GM8A 3AI9X 4YQ4A 1WRPR 5FAIA 1VHKA 2Z0YA 2V3KA 4YVJA 4YQ0A 3FRWA 1RCSA 1O6DA 2HA8A 1TO0A 4JWHA 3BBHA 1V6ZA 3N4JA 1JHGA 4MCCA 1NXZA 4YQ1A 4YQTA 4YQCA 3G1CA 4JWGA 3SSXN 2EGVA 4J3CA 4JWJA 4YQRA 2QWVA 3BBDA 1K3RA 5CO4A 3KW2A 1P9PA 1UALA 4JALA 1Z85A 1IPAA 3IC6A 1OY5A 4CNDA 3NK7A 1CO0A 4YQJA 2YY8A 4MCBA 2O3AA 4MCDA
chains in the Genus database with same CATH topology
3KY7A 3L8UA 1UAKA 4YPZA 4YVHA 4YPWA 4YQIA 1VH0A 4YQOA 3BBEA 2V3JA 3E5YA 4E8BA 3OINA 2CX8A 4YQ5A 4YPXA 3ILKA 1UAJA 5D9FA 3KNUA 3OIIA 4YQBA 1J85A 4KDZA 3O7BA 4X3LA 1X7OA 2QMMA 3IEFA 4YQLA 1MXIA 3AIAA 4YQQA 4YVIA 4XBOA 5GMBA 1GZ0A 4YQSA 3KTYA 4CNGA 1VHYA 4YQ9A 4JAKA 4YQ7A 4YQAA 4H3ZA 4FMWA 1ZJRA 4YQNA 4YQGA 3GYQA 4YQ3A 3OIJA 2I6DA 4KGNA 4IG6A 4L69A 4YVKA 2EGWA 4YPYA 4YQKA 1X7PA 1NS5A 3NK6A 3AXZA 4JWFA 4RG1A 4CNFA 4H3YA 4X3MA 3DCMX 4YQPA 4PZKA 3N4KA 1UAMA 4CNEA 4FAKA 4YQ6A 5GMCA 3QUVA 3ONPA 1V2XA 4YQ8A 4YVGA 4YQ2A 4YQDA 5GM8A 3AI9X 4YQ4A 5FAIA 1VHKA 2Z0YA 2V3KA 4YVJA 4YQ0A 1O6DA 2HA8A 1TO0A 4JWHA 3BBHA 1V6ZA 3N4JA 4MCCA 1NXZA 4YQ1A 4YQTA 4YQCA 4JWGA 2EGVA 4J3CA 4JWJA 4YQRA 2QWVA 3BBDA 1K3RA 5CO4A 3KW2A 1P9PA 1UALA 4JALA 1Z85A 1IPAA 3IC6A 1OY5A 4CNDA 3NK7A 4YQJA 2YY8A 4MCBA 2O3AA 4MCDA
chains in the Genus database with same CATH homology


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