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


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