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


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