4YVIA

Crystal structure of h. influenzae trmd in complex with sinefungin and trna
Total Genus 65
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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
65
Knots found
sequence length
247
structure length
239
Chain Sequence
HMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
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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 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)
molecule tags Transferase/rna
total genus 65
structure length 239
sequence length 247
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 4yviA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yviA01
3KTYA 4KDZA 4XBOA 5GMBA 4MCBA 2EGVA 3OIJA 3KY7A 4YQGA 3NK7A 4X3LA 4YQAA 3BBEA 1J85A 1V6ZA 4YQLA 4X3MA 2YY8A 4YQ1A 4CNGA 3OINA 4H3YA 4E8BA 3N4JA 1O6DA 2I6DA 3IC6A 4YQPA 4YQSA 1TO0A 4YVGA 4RG1A 4YQJA 2HA8A 1UAJA 3GYQA 3KNUA 1VH0A 4L69A 2CX8A 4YVKA 4YVHA 4J3CA 4YQIA 1IPAA 4YPXA 1NS5A 5D9FA 4YQ3A 1UAKA 2QWVA 4JAKA 1Z85A 3OIIA 4YQRA 4YQ8A 3E5YA 5FAIA 1UAMA 4YQCA 4YQNA 4YPYA 5GMCA 4MCDA 3AXZA 3KW2A 1ZJRA 4FAKA 4YPZA 4YQDA 4YQ4A 3IEFA 4YQOA 4MCCA 1MXIA 2EGWA 4YQ9A 1V2XA 1P9PA 3ONPA 4CNDA 4YQTA 1X7PA 3NK6A 4YQ5A 1VHYA 2QMMA 3DCMX 4YPWA 4YQ2A 1NXZA 4YVJA 3BBHA 3O7BA 3ILKA 4YQBA 3L8UA 2V3JA 1OY5A 4KGNA 4PZKA 5CO4A 1X7OA 2Z0YA 4YQKA 3AI9X 4CNFA 4YQ7A 1VHKA 4H3ZA 2V3KA 3AIAA 1GZ0A 5GM8A 4CNEA 3QUVA 4YVIA 4YQ0A 4YQQA 3N4KA 4IG6A 3BBDA 1UALA 2O3AA 4JALA 4YQ6A 1K3RA
chains in the Genus database with same CATH superfamily
3KTYA 4KDZA 1JHGA 4XBOA 5GMBA 4MCBA 2EGVA 1TROA 3OIJA 3KY7A 4YQGA 1RCSA 3NK7A 4X3LA 4YQAA 3KORA 3BBEA 1J85A 1V6ZA 4YQLA 4X3MA 2YY8A 1ZT9A 4YQ1A 4CNGA 3OINA 4H3YA 4JWJA 4E8BA 3N4JA 1O6DA 4JWGA 2I6DA 3IC6A 4YQPA 4YQSA 1TO0A 4YVGA 4RG1A 4YQJA 2HA8A 1UAJA 3GYQA 3KNUA 3SSWN 3FRWA 1VH0A 4JWHA 4L69A 2CX8A 4YVKA 4YVHA 4J3CA 1WRSR 4YQIA 1IPAA 1WRPR 4YPXA 1CO0A 1NS5A 5D9FA 4YQ3A 1UAKA 2QWVA 3G1CA 4JAKA 1Z85A 3OIIA 4YQRA 4YQ8A 3E5YA 5FAIA 1UAMA 4FMWA 4YQCA 4YQNA 4YPYA 5GMCA 4MCDA 3AXZA 2OZ9R 1ZJRA 3KW2A 4YPZA 4FAKA 4YQ4A 4YQDA 3IEFA 4YQOA 4MCCA 1MXIA 2EGWA 4YQ9A 4JWFA 1V2XA 1P9PA 3ONPA 4CNDA 4YQTA 1X7PA 1MI7R 3NK6A 4YQ5A 1VHYA 2QMMA 3DCMX 4YPWA 4YQ2A 1NXZA 4YVJA 3BBHA 3O7BA 3ILKA 4YQBA 3L8UA 2V3JA 1OY5A 4KGNA 4PZKA 5CO4A 1WRTR 1X7OA 2XDIA 2Z0YA 4YQKA 3AI9X 4CNFA 4YQ7A 1VHKA 4H3ZA 2V3KA 3SSXN 3AIAA 1GZ0A 5GM8A 1TRRA 4CNEA 3WRPA 3QUVA 4YVIA 4YQ0A 4YQQA 3N4KA 4IG6A 3BBDA 1UALA 2O3AA 4JALA 4YQ6A 1K3RA
chains in the Genus database with same CATH topology
3KTYA 4KDZA 4XBOA 5GMBA 4MCBA 2EGVA 3OIJA 3KY7A 4YQGA 3NK7A 4X3LA 4YQAA 3BBEA 1J85A 1V6ZA 4YQLA 4X3MA 2YY8A 4YQ1A 4CNGA 3OINA 4H3YA 4JWJA 4E8BA 3N4JA 1O6DA 4JWGA 2I6DA 3IC6A 4YQPA 4YQSA 1TO0A 4YVGA 4RG1A 4YQJA 2HA8A 1UAJA 3GYQA 3KNUA 1VH0A 4JWHA 4L69A 2CX8A 4YVKA 4YVHA 4J3CA 4YQIA 1IPAA 4YPXA 1NS5A 5D9FA 4YQ3A 1UAKA 2QWVA 4JAKA 1Z85A 3OIIA 4YQRA 4YQ8A 3E5YA 5FAIA 1UAMA 4FMWA 4YQCA 4YQNA 4YPYA 5GMCA 4MCDA 3AXZA 3KW2A 1ZJRA 4FAKA 4YPZA 4YQDA 4YQ4A 3IEFA 4YQOA 4MCCA 1MXIA 2EGWA 4YQ9A 4JWFA 1V2XA 1P9PA 3ONPA 4CNDA 4YQTA 1X7PA 3NK6A 4YQ5A 1VHYA 2QMMA 3DCMX 4YPWA 4YQ2A 1NXZA 4YVJA 3BBHA 3O7BA 3ILKA 4YQBA 3L8UA 2V3JA 1OY5A 4KGNA 4PZKA 5CO4A 1X7OA 2Z0YA 4YQKA 3AI9X 4CNFA 4YQ7A 1VHKA 4H3ZA 2V3KA 3AIAA 1GZ0A 5GM8A 4CNEA 3QUVA 4YVIA 4YQ0A 4YQQA 3N4KA 4IG6A 3BBDA 1UALA 2O3AA 4JALA 4YQ6A 1K3RA
chains in the Genus database with same CATH homology


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