4YVGA

Crystal structure of h. influenzae trmd in complex with adomet
Total Genus 77
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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
77
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 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 77
structure length 239
sequence length 247
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 4yvgA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yvgA01
2EGWA 1O6DA 3ONPA 3OIJA 1IPAA 5GM8A 4YQPA 1UAJA 5GMCA 2HA8A 1X7OA 4YQRA 3ILKA 4H3YA 3L8UA 4YPXA 3AIAA 1UAMA 4E8BA 4YQ9A 4YPYA 4YQJA 4X3LA 2V3KA 3BBHA 4CNFA 2YY8A 4YQIA 2O3AA 1GZ0A 1VHYA 4YQKA 4YQ2A 4YQ1A 3KNUA 4XBOA 3N4KA 2V3JA 1J85A 5FAIA 4YQ6A 1Z85A 1P9PA 2Z0YA 3E5YA 1V6ZA 2QMMA 4KGNA 5GMBA 3O7BA 1V2XA 4YPZA 2I6DA 2EGVA 3BBDA 2QWVA 4YVJA 4YQTA 1ZJRA 4YQOA 4YQ3A 4YQ8A 4YVKA 3OINA 5CO4A 3KY7A 4CNDA 4YQLA 1OY5A 1VH0A 3BBEA 4MCDA 4YQBA 1UALA 4IG6A 3KW2A 4KDZA 3GYQA 4CNEA 1NS5A 1NXZA 4RG1A 4YVHA 3IC6A 3DCMX 4MCBA 4YQCA 4L69A 3IEFA 4YVGA 1UAKA 5D9FA 1TO0A 4YQSA 4J3CA 1X7PA 4YQAA 1VHKA 2CX8A 4X3MA 4JAKA 3OIIA 4YQNA 3QUVA 4YQDA 4CNGA 4YQ4A 4YQ5A 3KTYA 4YQGA 1MXIA 4MCCA 4YQ0A 4YQ7A 3AI9X 4H3ZA 3AXZA 4YQQA 1K3RA 4JALA 3NK6A 3N4JA 4PZKA 4YVIA 4YPWA 4FAKA 3NK7A
chains in the Genus database with same CATH superfamily
2EGWA 1O6DA 3ONPA 3OIJA 1IPAA 5GM8A 4YQPA 4JWJA 1UAJA 3WRPA 5GMCA 2HA8A 1WRTR 1X7OA 1MI7R 4YQRA 4H3YA 3ILKA 3L8UA 2OZ9R 4YPXA 3AIAA 1UAMA 4E8BA 4YQ9A 4YPYA 4YQJA 4X3LA 2V3KA 3G1CA 1TROA 3BBHA 4CNFA 2YY8A 4YQIA 2O3AA 1GZ0A 4JWHA 1VHYA 4YQKA 4YQ2A 3SSWN 4YQ1A 3KNUA 4XBOA 2XDIA 3N4KA 2V3JA 1J85A 5FAIA 4YQ6A 1Z85A 1ZT9A 1P9PA 2Z0YA 3E5YA 4JWGA 1V6ZA 3FRWA 2QMMA 4KGNA 5GMBA 3O7BA 1WRPR 4YPZA 1V2XA 2EGVA 2I6DA 2QWVA 3BBDA 4YVJA 4YQTA 1ZJRA 4YQOA 4YQ3A 4YQ8A 4YVKA 3OINA 5CO4A 3KY7A 4CNDA 4YQLA 1OY5A 1VH0A 3BBEA 4MCDA 4YQBA 1UALA 3KORA 4IG6A 3KW2A 4KDZA 3GYQA 4CNEA 1TRRA 1NS5A 1NXZA 4FMWA 4RG1A 4YVHA 3IC6A 3DCMX 4JWFA 4MCBA 4YQCA 4L69A 3IEFA 4YVGA 1UAKA 5D9FA 1TO0A 4YQSA 4J3CA 1X7PA 4YQAA 1RCSA 1VHKA 2CX8A 1CO0A 4X3MA 4JAKA 3OIIA 4YQNA 3QUVA 4YQDA 4CNGA 4YQ4A 4YQ5A 3KTYA 4YQGA 3SSXN 1MXIA 4MCCA 4YQ0A 4YQ7A 3AI9X 1WRSR 4H3ZA 3AXZA 1JHGA 4YQQA 1K3RA 4JALA 3NK6A 3N4JA 4PZKA 4YVIA 4YPWA 4FAKA 3NK7A
chains in the Genus database with same CATH topology
2EGWA 1O6DA 3ONPA 3OIJA 1IPAA 5GM8A 4YQPA 4JWJA 1UAJA 5GMCA 2HA8A 1X7OA 4YQRA 3ILKA 4H3YA 3L8UA 4YPXA 3AIAA 1UAMA 4E8BA 4YQ9A 4YPYA 4YQJA 4X3LA 2V3KA 3BBHA 4CNFA 2YY8A 4YQIA 2O3AA 1GZ0A 4JWHA 1VHYA 4YQKA 4YQ2A 4YQ1A 3KNUA 4XBOA 3N4KA 2V3JA 1J85A 5FAIA 4YQ6A 1Z85A 1P9PA 2Z0YA 3E5YA 4JWGA 1V6ZA 2QMMA 4KGNA 5GMBA 3O7BA 1V2XA 4YPZA 2I6DA 2EGVA 3BBDA 2QWVA 4YVJA 4YQTA 1ZJRA 4YQOA 4YQ3A 4YQ8A 4YVKA 3OINA 5CO4A 3KY7A 4CNDA 4YQLA 1OY5A 1VH0A 3BBEA 4MCDA 4YQBA 1UALA 4IG6A 3KW2A 4KDZA 3GYQA 4CNEA 1NS5A 1NXZA 4FMWA 4RG1A 4YVHA 3IC6A 3DCMX 4JWFA 4MCBA 4YQCA 4L69A 3IEFA 4YVGA 1UAKA 5D9FA 1TO0A 4YQSA 4J3CA 1X7PA 4YQAA 1VHKA 2CX8A 4X3MA 4JAKA 3OIIA 4YQNA 3QUVA 4YQDA 4CNGA 4YQ4A 4YQ5A 3KTYA 4YQGA 1MXIA 4MCCA 4YQ0A 4YQ7A 3AI9X 4H3ZA 3AXZA 4YQQA 1K3RA 4JALA 3NK6A 3N4JA 4PZKA 4YVIA 4YPWA 4FAKA 3NK7A
chains in the Genus database with same CATH homology


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