4YVHA

Crystal structure of h. influenzae trmd in complex with sinefungin
Total Genus 74
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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
74
Knots found
sequence length
248
structure length
240
Chain Sequence
SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
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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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publication title Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
pubmed doi rcsb
molecule tags Transferase
source organism Haemophilus influenzae (strain atcc 51907 / dsm 11121 / kw20 / rd)
molecule keywords tRNA (guanine-N(1)-)-methyltransferase
total genus 74
structure length 240
sequence length 248
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 4yvhA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yvhA01
4H3YA 3BBDA 3KY7A 2EGVA 3IEFA 3ILKA 1TO0A 4KGNA 2HA8A 4JALA 1ZJRA 3KW2A 1VH0A 3OIIA 4MCBA 4YQTA 4X3LA 3BBEA 3E5YA 4KDZA 1NXZA 4YQ7A 4CNFA 1MXIA 4YQDA 4YQAA 4FAKA 1UAJA 4YQLA 1X7OA 2Z0YA 4YPZA 3AI9X 4PZKA 4YPWA 4YVHA 3AXZA 3KTYA 3ONPA 4YQ1A 4YQIA 4RG1A 4YQ6A 5FAIA 1J85A 5GMBA 4YVIA 3OIJA 1GZ0A 4YQOA 3NK6A 4MCCA 1O6DA 4MCDA 3NK7A 4YQPA 1X7PA 4CNGA 4YQ2A 5CO4A 2V3KA 4CNDA 4YQQA 5GM8A 1Z85A 4JAKA 1IPAA 3DCMX 3BBHA 3KNUA 1P9PA 4YQRA 4YQSA 4H3ZA 4XBOA 4YQ9A 2QMMA 4YQ5A 5GMCA 4E8BA 3IC6A 2YY8A 3L8UA 1V2XA 4YQ0A 1OY5A 4YQJA 3N4JA 4YQ4A 2EGWA 4CNEA 3N4KA 1UAMA 2QWVA 3O7BA 3OINA 1UALA 4YQCA 4YVGA 4YVKA 1K3RA 2O3AA 2V3JA 4YPXA 4YQGA 3QUVA 4YQBA 3AIAA 5D9FA 4YQ8A 4J3CA 1V6ZA 4IG6A 4YQKA 1UAKA 1VHYA 3GYQA 4YVJA 4YQNA 1NS5A 4X3MA 2I6DA 4YPYA 4YQ3A 4L69A 2CX8A 1VHKA
chains in the Genus database with same CATH superfamily
4H3YA 3BBDA 3KY7A 3WRPA 2EGVA 3IEFA 3ILKA 1TO0A 1TRRA 4KGNA 2HA8A 4JALA 4JWHA 2XDIA 1JHGA 1ZJRA 3KW2A 1VH0A 3OIIA 4MCBA 4YQTA 4JWJA 4X3LA 3BBEA 3E5YA 4KDZA 1NXZA 4YQ7A 4CNFA 1MXIA 4YQDA 4YQAA 1RCSA 1WRTR 4FAKA 1UAJA 4YQLA 1X7OA 2Z0YA 4YPZA 3AI9X 4PZKA 4YPWA 4YVHA 3AXZA 3KTYA 3ONPA 4YQ1A 4YQIA 1MI7R 4RG1A 4YQ6A 5FAIA 1J85A 5GMBA 3OIJA 1GZ0A 4YQOA 3NK6A 4MCCA 1O6DA 4MCDA 3NK7A 4YQPA 1WRPR 1X7PA 4CNGA 3KORA 4YQ2A 5CO4A 3FRWA 2V3KA 4CNDA 4YQQA 5GM8A 1Z85A 4JAKA 1IPAA 3DCMX 2OZ9R 3BBHA 1ZT9A 2CX8A 4JWFA 3KNUA 1P9PA 4YQRA 4YQSA 4H3ZA 4XBOA 4YQ9A 2QMMA 4YQ5A 5GMCA 4E8BA 3IC6A 2YY8A 3G1CA 3L8UA 1V2XA 4YQ0A 1OY5A 4YQJA 3N4JA 1WRSR 4YQ4A 2EGWA 4CNEA 3N4KA 1UAMA 2QWVA 3O7BA 3OINA 1UALA 4YQCA 4YVGA 1TROA 4YVKA 1CO0A 1K3RA 2O3AA 2V3JA 4FMWA 4JWGA 4YPXA 4YQGA 3SSWN 3QUVA 3SSXN 4YQBA 3AIAA 5D9FA 4YQ8A 4J3CA 1V6ZA 4IG6A 4YQKA 1UAKA 1VHYA 3GYQA 4YVJA 4YQNA 1NS5A 4X3MA 2I6DA 4YPYA 4YQ3A 4L69A 4YVIA 1VHKA
chains in the Genus database with same CATH topology
4H3YA 3BBDA 3KY7A 2EGVA 3IEFA 3ILKA 1TO0A 4KGNA 2HA8A 4JALA 4JWHA 1ZJRA 3KW2A 1VH0A 3OIIA 4MCBA 4YQTA 4JWJA 4X3LA 3BBEA 3E5YA 4KDZA 1NXZA 4YQ7A 4CNFA 1MXIA 4YQDA 4YQAA 4FAKA 1UAJA 4YQLA 1X7OA 2Z0YA 4YPZA 3AI9X 4PZKA 4YPWA 4YVHA 3AXZA 3KTYA 3ONPA 4YQ1A 4YQIA 4RG1A 4YQ6A 5FAIA 1J85A 5GMBA 4YVIA 3OIJA 1GZ0A 4YQOA 3NK6A 4MCCA 1O6DA 4MCDA 3NK7A 4YQPA 1X7PA 4CNGA 4YQ2A 5CO4A 2V3KA 4CNDA 4YQQA 5GM8A 1Z85A 4JAKA 1IPAA 3DCMX 3BBHA 4JWFA 3KNUA 1P9PA 4YQRA 4YQSA 4H3ZA 4XBOA 4YQ9A 2QMMA 4YQ5A 5GMCA 4E8BA 3IC6A 2YY8A 3L8UA 1V2XA 4YQ0A 1OY5A 4YQJA 3N4JA 4YQ4A 2EGWA 4CNEA 3N4KA 1UAMA 2QWVA 3O7BA 3OINA 1UALA 4YQCA 4YVGA 4YVKA 1K3RA 2O3AA 2V3JA 4FMWA 4JWGA 4YPXA 4YQGA 3QUVA 4YQBA 3AIAA 5D9FA 4YQ8A 4J3CA 1V6ZA 4IG6A 4YQKA 1UAKA 1VHYA 3GYQA 4YVJA 4YQNA 1NS5A 4X3MA 2I6DA 4YPYA 4YQ3A 4L69A 2CX8A 1VHKA
chains in the Genus database with same CATH homology


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