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


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