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


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