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


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