4YVKA

Crystal structure of h. influenzae trmd in complex with sinefungin and trna variant (g36c)
Total Genus 68
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
68
Knots found
sequence length
248
structure length
239
Chain Sequence
SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
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) }}
molecule tags Transferase/rna
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 68
structure length 239
sequence length 248
chains with identical sequence B
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 4yvkA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yvkA01
1UAJA 4X3MA 4MCBA 4YQ2A 4CNGA 1X7OA 1Z85A 3OINA 4YQCA 2V3JA 4YQ3A 5GMCA 4YQOA 4YQ0A 4YQ8A 1UAKA 4YQ7A 2CX8A 3KY7A 1V2XA 4CNEA 2EGVA 1NXZA 4YQPA 4YQIA 4YPXA 4YPWA 1V6ZA 1VHKA 5D9FA 2Z0YA 4L69A 3AIAA 4YQ1A 3AI9X 4YQGA 1UAMA 4YQJA 4YQNA 3AXZA 1MXIA 2EGWA 4YQQA 3ONPA 4MCDA 3BBDA 4KDZA 4YQSA 4H3YA 4YVGA 5CO4A 4H3ZA 4E8BA 4XBOA 4YQDA 1OY5A 3KTYA 4KGNA 3OIIA 4YVIA 3E5YA 1IPAA 4YQKA 1P9PA 2I6DA 3QUVA 4YQAA 2QWVA 4YQBA 4IG6A 3BBHA 1UALA 3OIJA 4JALA 4MCCA 3N4KA 4CNDA 1J85A 1O6DA 4PZKA 3KNUA 3O7BA 4CNFA 4YVJA 3NK7A 5GMBA 3IC6A 3GYQA 1VH0A 2YY8A 1GZ0A 5GM8A 3IEFA 4YQLA 1ZJRA 3ILKA 4JAKA 4YPYA 5FAIA 4J3CA 4YQ9A 3KW2A 4YVKA 2QMMA 4FAKA 4RG1A 4YVHA 4YQRA 4YPZA 4YQ4A 4YQ5A 1NS5A 2V3KA 4YQ6A 1K3RA 3DCMX 3BBEA 1X7PA 4X3LA 2HA8A 1VHYA 1TO0A 2O3AA 3N4JA 3L8UA 4YQTA 3NK6A
chains in the Genus database with same CATH superfamily
1UAJA 4X3MA 4MCBA 4YQ2A 4CNGA 1TRRA 1X7OA 1Z85A 3OINA 4YQCA 2V3JA 4YQ3A 5GMCA 4YQOA 1TROA 4YQ0A 4FMWA 4YQ8A 1UAKA 4YQ7A 2CX8A 3KY7A 1V2XA 4CNEA 2EGVA 1NXZA 4YQPA 3SSWN 4YQIA 4YPXA 4YPWA 1V6ZA 2XDIA 1VHKA 1JHGA 5D9FA 2Z0YA 4L69A 3AIAA 4YQ1A 3AI9X 4YQGA 1UAMA 4YQJA 4YQNA 3AXZA 1MXIA 2EGWA 4YQQA 3ONPA 4MCDA 1ZT9A 3BBDA 4KDZA 4JWHA 4JWGA 4YQSA 4H3YA 4YVGA 5CO4A 4H3ZA 4E8BA 4XBOA 1WRPR 4YQDA 1OY5A 3KTYA 4KGNA 3OIIA 4YVIA 3E5YA 1IPAA 4YQKA 1P9PA 2I6DA 3QUVA 2OZ9R 4YQAA 2QWVA 4YQBA 4IG6A 3BBHA 1UALA 3OIJA 4JALA 3G1CA 4MCCA 3SSXN 3N4KA 4CNDA 1J85A 1O6DA 3WRPA 4PZKA 1WRTR 1RCSA 3KNUA 3O7BA 4CNFA 4YVJA 3NK7A 1CO0A 5GMBA 3IC6A 3GYQA 1VH0A 2YY8A 1GZ0A 1WRSR 3IEFA 3FRWA 4YQLA 1ZJRA 5GM8A 3ILKA 4JAKA 4YPYA 5FAIA 4J3CA 4YQ9A 3KW2A 4YVKA 2QMMA 4FAKA 4RG1A 4JWJA 4YVHA 4YQRA 1MI7R 4YPZA 4YQ4A 4YQ5A 1NS5A 4JWFA 2V3KA 4YQ6A 1K3RA 3KORA 3BBEA 3DCMX 1X7PA 4X3LA 2HA8A 1VHYA 1TO0A 2O3AA 3N4JA 3L8UA 4YQTA 3NK6A
chains in the Genus database with same CATH topology
1UAJA 4X3MA 4MCBA 4YQ2A 4CNGA 1X7OA 1Z85A 3OINA 4YQCA 2V3JA 4YQ3A 5GMCA 4YQOA 4YQ0A 4FMWA 4YQ8A 1UAKA 4YQ7A 2CX8A 3KY7A 1V2XA 4CNEA 2EGVA 1NXZA 4YQPA 4YQIA 4YPXA 4YPWA 1V6ZA 1VHKA 5D9FA 2Z0YA 4L69A 3AIAA 4YQ1A 3AI9X 4YQGA 1UAMA 4YQJA 4YQNA 3AXZA 1MXIA 2EGWA 4YQQA 3ONPA 4MCDA 3BBDA 4KDZA 4JWHA 4JWGA 4YQSA 4H3YA 4YVGA 5CO4A 4H3ZA 4E8BA 4XBOA 4YQDA 1OY5A 3KTYA 4KGNA 3OIIA 4YVIA 3E5YA 1IPAA 4YQKA 1P9PA 2I6DA 3QUVA 4YQAA 2QWVA 4YQBA 4IG6A 3BBHA 1UALA 3OIJA 4JALA 4MCCA 3N4KA 4CNDA 1J85A 1O6DA 4PZKA 3KNUA 3O7BA 4CNFA 4YVJA 3NK7A 5GMBA 3IC6A 3GYQA 1VH0A 2YY8A 1GZ0A 5GM8A 3IEFA 4YQLA 1ZJRA 3ILKA 4JAKA 4YPYA 5FAIA 4J3CA 4YQ9A 3KW2A 4YVKA 2QMMA 4FAKA 4RG1A 4JWJA 4YVHA 4YQRA 4YPZA 4YQ4A 4YQ5A 1NS5A 4JWFA 2V3KA 4YQ6A 1K3RA 3DCMX 3BBEA 1X7PA 4X3LA 2HA8A 1VHYA 1TO0A 2O3AA 3N4JA 3L8UA 4YQTA 3NK6A
chains in the Genus database with same CATH homology


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