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


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