4YVKA

Crystal structure of h. influenzae trmd in complex with sinefungin and trna variant (g36c)
Total Genus 68
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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
68
Knots found
sequence length
248
structure length
239
Chain Sequence
SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
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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 68
structure length 239
sequence length 248
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 4yvkA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yvkA01
4YQKA 1ZJRA 3ILKA 5D9FA 3GYQA 3KTYA 4CNEA 1MXIA 1VHKA 2QWVA 4YQOA 1V2XA 5FAIA 4YPZA 4YVKA 4YQBA 4MCDA 4KGNA 3BBHA 4PZKA 3KNUA 1NXZA 3KY7A 4KDZA 4YVGA 4YQ5A 4YQSA 3BBDA 4YQGA 5CO4A 4YPYA 4YQTA 4YQ4A 3ONPA 1UAJA 4YVHA 4YVJA 4MCBA 4YQIA 2EGWA 1NS5A 4YQQA 1GZ0A 3N4KA 3NK7A 3N4JA 1UALA 3OIJA 1V6ZA 4JALA 4YQDA 4H3YA 3L8UA 1X7PA 4YQRA 3DCMX 4FAKA 1VH0A 2O3AA 4X3MA 1X7OA 4CNDA 4H3ZA 3IEFA 1O6DA 4X3LA 3AIAA 1K3RA 4YQPA 2I6DA 4CNFA 1IPAA 3BBEA 4L69A 4YQ0A 5GMBA 3NK6A 3O7BA 4YQ2A 4J3CA 2YY8A 2V3KA 5GMCA 2V3JA 1P9PA 4IG6A 4YVIA 4RG1A 3OIIA 4YQ9A 5GM8A 1UAMA 3AI9X 4YQCA 4YQJA 4YQ3A 4YPWA 2QMMA 4YQLA 3KW2A 3AXZA 4YQ7A 4CNGA 1UAKA 1TO0A 1OY5A 2CX8A 1VHYA 4YQNA 3E5YA 3IC6A 2EGVA 1J85A 4YQ6A 4YQ8A 4E8BA 3OINA 1Z85A 4MCCA 4JAKA 3QUVA 2HA8A 4YPXA 4YQAA 2Z0YA 4YQ1A 4XBOA
chains in the Genus database with same CATH superfamily
4YQKA 1ZJRA 3G1CA 3ILKA 5D9FA 3GYQA 3KTYA 4FMWA 4CNEA 1MXIA 1VHKA 1WRPR 4YQOA 1V2XA 2QWVA 5FAIA 4YPZA 4YVKA 4YQBA 2XDIA 4MCDA 4KGNA 3BBHA 3KORA 4PZKA 3KNUA 1NXZA 3KY7A 2OZ9R 4KDZA 4YVGA 4YQ5A 4YQSA 3BBDA 4YQGA 5CO4A 4YPYA 4YQTA 4YQ4A 3ONPA 1UAJA 4YVHA 4YVJA 1WRSR 4MCBA 4YQIA 2EGWA 1NS5A 4YQQA 1GZ0A 1CO0A 3N4KA 3NK7A 3N4JA 1UALA 3OIJA 1V6ZA 4JALA 4YQDA 4H3YA 3L8UA 1X7PA 4YQRA 3DCMX 4JWFA 4FAKA 1VH0A 2O3AA 4X3MA 1X7OA 4CNDA 4H3ZA 3IEFA 1O6DA 4X3LA 3AIAA 1K3RA 4YQPA 3FRWA 2I6DA 4CNFA 1IPAA 3BBEA 4L69A 4YQ0A 1JHGA 5GMBA 3NK6A 3O7BA 4YQ2A 4J3CA 1WRTR 4JWHA 2YY8A 2V3KA 5GMCA 2V3JA 1P9PA 4IG6A 3SSXN 4YVIA 4RG1A 1TROA 3OIIA 1RCSA 4YQ9A 5GM8A 1UAMA 3AI9X 4YQCA 4YQJA 1ZT9A 4JWJA 4YQ3A 4YPWA 2QMMA 4YQLA 3KW2A 3AXZA 4YQ7A 4CNGA 1UAKA 1TO0A 1OY5A 2CX8A 1VHYA 4YQNA 3E5YA 3IC6A 2EGVA 1J85A 4YQ6A 4YQ8A 3SSWN 1MI7R 4E8BA 3OINA 1Z85A 4MCCA 1TRRA 4JAKA 4JWGA 3QUVA 2HA8A 4YPXA 4YQAA 2Z0YA 4YQ1A 3WRPA 4XBOA
chains in the Genus database with same CATH topology
4YQKA 1ZJRA 3ILKA 5D9FA 3GYQA 3KTYA 4FMWA 4CNEA 1MXIA 1VHKA 2QWVA 4YQOA 1V2XA 5FAIA 4YPZA 4YVKA 4YQBA 4MCDA 4KGNA 3BBHA 4PZKA 3KNUA 1NXZA 3KY7A 4KDZA 4YVGA 4YQ5A 4YQSA 3BBDA 4YQGA 5CO4A 4YPYA 4YQTA 4YQ4A 3ONPA 1UAJA 4YVHA 4YVJA 4MCBA 4YQIA 2EGWA 1NS5A 4YQQA 1GZ0A 3N4KA 3NK7A 3N4JA 1UALA 3OIJA 1V6ZA 4JALA 4YQDA 4H3YA 3L8UA 1X7PA 4YQRA 3DCMX 4JWFA 4FAKA 1VH0A 2O3AA 4X3MA 1X7OA 4CNDA 4H3ZA 3IEFA 1O6DA 4X3LA 3AIAA 1K3RA 4YQPA 2I6DA 4CNFA 1IPAA 3BBEA 4L69A 4YQ0A 5GMBA 3NK6A 3O7BA 4YQ2A 4J3CA 4JWHA 2YY8A 2V3KA 5GMCA 2V3JA 1P9PA 4IG6A 4YVIA 4RG1A 3OIIA 4YQ9A 5GM8A 1UAMA 3AI9X 4YQCA 4YQJA 4JWJA 4YQ3A 4YPWA 2QMMA 4YQLA 3KW2A 3AXZA 4YQ7A 4CNGA 1UAKA 1TO0A 1OY5A 2CX8A 1VHYA 4YQNA 3E5YA 3IC6A 2EGVA 1J85A 4YQ6A 4YQ8A 4E8BA 3OINA 1Z85A 4MCCA 4JAKA 4JWGA 3QUVA 2HA8A 4YPXA 4YQAA 2Z0YA 4YQ1A 4XBOA
chains in the Genus database with same CATH homology


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