4YVHA

Crystal structure of h. influenzae trmd in complex with sinefungin
Total Genus 74
Loading diagram...

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
Loading diagram...

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
{{ tooltip.sname }} connected with {{ tooltip.tname }} : {{qFormat(tooltip.svalue) }}
publication title Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
pubmed doi rcsb
molecule tags Transferase
source organism Haemophilus influenzae (strain atcc 51907 / dsm 11121 / kw20 / rd)
molecule keywords tRNA (guanine-N(1)-)-methyltransferase
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
3KW2A 3IEFA 4CNGA 1V6ZA 4JAKA 4YQIA 4JALA 3OINA 4YQJA 1Z85A 4J3CA 1MXIA 4XBOA 4YQ1A 1VHKA 4PZKA 2QWVA 1NXZA 3N4JA 3NK7A 3NK6A 5GM8A 4YQPA 2O3AA 2YY8A 3AXZA 4YPXA 4YVJA 4H3ZA 1J85A 3OIIA 4MCBA 4YQDA 3KNUA 2Z0YA 1V2XA 2HA8A 5GMBA 1NS5A 4YPZA 3AI9X 1IPAA 1OY5A 4YQ9A 5CO4A 1K3RA 4YQ6A 4YVKA 4KDZA 4YPWA 4CNEA 1X7OA 3BBHA 4YQLA 4YQGA 4YQ4A 1ZJRA 2EGVA 3L8UA 1UAMA 4YVHA 4YQOA 1UALA 4YQTA 4H3YA 4IG6A 4RG1A 3IC6A 3QUVA 2V3JA 1GZ0A 1TO0A 4FAKA 4YQ5A 3DCMX 2QMMA 4KGNA 4YQ3A 3O7BA 3E5YA 3KTYA 5FAIA 4YQNA 4MCDA 4YQ2A 2I6DA 4L69A 4CNDA 4YQSA 1UAJA 4YQ8A 4YQ0A 4YVIA 2V3KA 3GYQA 4YQAA 1VH0A 3ONPA 1X7PA 4X3LA 4YPYA 4MCCA 5D9FA 3BBDA 5GMCA 3BBEA 1UAKA 4YQRA 4X3MA 3ILKA 4YQQA 4CNFA 4YQ7A 3OIJA 3AIAA 1VHYA 3N4KA 2CX8A 4YQKA 4E8BA 4YVGA 1P9PA 2EGWA 1O6DA 4YQCA 3KY7A 4YQBA
chains in the Genus database with same CATH superfamily
1WRSR 3KW2A 3IEFA 4CNGA 1WRTR 1V6ZA 4YQIA 4JAKA 4JWFA 4JALA 3OINA 4YQJA 1Z85A 4J3CA 1MXIA 4XBOA 4YQ1A 1VHKA 4PZKA 2QWVA 1NXZA 3N4JA 3NK7A 3G1CA 3NK6A 5GM8A 4YQPA 2O3AA 2YY8A 3AXZA 4YPXA 1MI7R 4YVJA 3WRPA 4H3ZA 1J85A 3OIIA 4MCBA 4YQDA 3KNUA 2Z0YA 1V2XA 2HA8A 2OZ9R 5GMBA 1NS5A 4YPZA 3AI9X 1ZT9A 1IPAA 1OY5A 4YQ9A 5CO4A 1K3RA 4YQ6A 1CO0A 1RCSA 4YVKA 4KDZA 4YPWA 4CNEA 1X7OA 3SSWN 3BBHA 4YQLA 4YQGA 3SSXN 4YQ4A 1ZJRA 2EGVA 3L8UA 1UAMA 4YVHA 4FMWA 4YQOA 1UALA 4YQTA 4H3YA 4IG6A 4RG1A 3IC6A 3QUVA 2V3JA 1GZ0A 1JHGA 1TO0A 4FAKA 4YQ5A 3DCMX 4JWJA 2QMMA 4KGNA 4YQ3A 3O7BA 3E5YA 3KTYA 5FAIA 4YQNA 1TROA 4MCDA 4YQ2A 2I6DA 4L69A 4CNDA 4YQSA 1UAJA 4YQ8A 4YQ0A 4YVIA 2V3KA 3GYQA 4YQAA 1VH0A 3ONPA 1X7PA 4X3LA 4JWGA 4YPYA 4MCCA 5D9FA 3BBDA 5GMCA 3BBEA 1UAKA 4YQRA 4X3MA 3ILKA 4YQQA 1TRRA 4CNFA 4YQ7A 2XDIA 3OIJA 1WRPR 3KORA 3AIAA 1VHYA 3N4KA 2CX8A 4YQKA 4E8BA 4YVGA 1P9PA 2EGWA 3FRWA 4JWHA 1O6DA 4YQCA 3KY7A 4YQBA
chains in the Genus database with same CATH topology
3KW2A 3IEFA 4CNGA 1V6ZA 4JAKA 4YQIA 4JWFA 4JALA 3OINA 4YQJA 1Z85A 4J3CA 1MXIA 4XBOA 4YQ1A 1VHKA 4PZKA 2QWVA 1NXZA 3N4JA 3NK7A 3NK6A 5GM8A 4YQPA 2O3AA 2YY8A 3AXZA 4YPXA 4YVJA 4H3ZA 1J85A 3OIIA 4MCBA 4YQDA 3KNUA 2Z0YA 1V2XA 2HA8A 5GMBA 1NS5A 4YPZA 3AI9X 1IPAA 1OY5A 4YQ9A 5CO4A 1K3RA 4YQ6A 4YVKA 4KDZA 4YPWA 4CNEA 1X7OA 3BBHA 4YQLA 4YQGA 4YQ4A 1ZJRA 2EGVA 3L8UA 1UAMA 4YVHA 4FMWA 4YQOA 1UALA 4YQTA 4H3YA 4IG6A 4RG1A 3IC6A 3QUVA 2V3JA 1GZ0A 1TO0A 4FAKA 4YQ5A 3DCMX 4JWJA 2QMMA 4KGNA 4YQ3A 3O7BA 3E5YA 3KTYA 5FAIA 4YQNA 4MCDA 4YQ2A 2I6DA 4L69A 4CNDA 4YQSA 1UAJA 4YQ8A 4YQ0A 4YVIA 2V3KA 3GYQA 4YQAA 1VH0A 3ONPA 1X7PA 4X3LA 4JWGA 4YPYA 4MCCA 5D9FA 3BBDA 5GMCA 3BBEA 1UAKA 4YQRA 4X3MA 3ILKA 4YQQA 4CNFA 4YQ7A 3OIJA 3AIAA 1VHYA 3N4KA 2CX8A 4YQKA 4E8BA 4YVGA 1P9PA 2EGWA 4JWHA 1O6DA 4YQCA 3KY7A 4YQBA
chains in the Genus database with same CATH homology


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...