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


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