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


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