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


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