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


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