4YQDA

Crystal structure of trmd, a m1g37 trna methyltransferase with sam-competitive compounds
Total Genus 70
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
70
Knots found
sequence length
249
structure length
244
Chain Sequence
b'GSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGASASFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS'
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 keywords tRNA (guanine-N(1)-)-methyltransferase
publication title Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
rcsb
source organism Haemophilus influenzae (strain atcc 51907 / dsm 11121 / kw20 / rd)
molecule tags Transferase/transferase inhibitor
total genus 70
structure length 244
sequence length 249
other databases KnotProt 2.0: K +31
ec nomenclature ec 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
pdb deposition date 2015-03-13

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 4yqdA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yqdA01
4YQ1A 4RG1A 4YQOA 3N4JA 4YQ7A 4MCCA 4KGNA 1MXIA 1OY5A 4KDZA 4E8BA 4YQ5A 3ONPA 2YY8A 3IEFA 3OIIA 3BBDA 4YQKA 1ZJRA 3GYQA 3AXZA 3KY7A 2V3KA 2I6DA 5GMBA 1X7OA 4YQ9A 1Z85A 1K3RA 4YQTA 2Z0YA 4YQ8A 1TO0A 3IC6A 3KW2A 3OIJA 1UALA 5D9FA 2EGVA 5GMCA 4YQSA 4YQLA 2HA8A 3KNUA 4MCBA 1UAKA 2EGWA 4YVGA 4MCDA 3NK7A 1IPAA 1GZ0A 1UAJA 3O7BA 4YQ3A 4YVIA 3KTYA 4CNFA 4XBOA 4YPZA 3AIAA 4JALA 4YQBA 3OINA 4X3MA 2QWVA 4YQQA 1V6ZA 4L69A 4CNDA 4JAKA 4YQAA 2O3AA 3DCMX 4IG6A 3QUVA 4X3LA 1X7PA 4YVKA 4YPWA 3L8UA 4YQ0A 4YQ6A 1UAMA 4YQCA 2CX8A 4CNEA 5CO4A 1VH0A 4J3CA 4PZKA 4YQDA 4YQ4A 4YVJA 3AI9X 1O6DA 4YQGA 1V2XA 2V3JA 1VHKA 4FAKA 4YQPA 1NXZA 4CNGA 4YVHA 4H3ZA 1NS5A 2QMMA 1VHYA 3N4KA 5GM8A 3BBEA 4YQNA 5FAIA 4YQRA 4YPYA 4YPXA 3NK6A 4H3YA 3BBHA 3E5YA 1J85A 4YQIA 4YQJA 3ILKA 4YQ2A 1P9PA
chains in the Genus database with same CATH superfamily
3FRWA 4YQ1A 4RG1A 4YQOA 3N4JA 4YQ7A 4MCCA 4KGNA 1WRSR 1MXIA 3WRPA 1OY5A 4KDZA 4E8BA 4YQ5A 3ONPA 2YY8A 3IEFA 3OIIA 3BBDA 4YQKA 1ZJRA 3GYQA 3AXZA 3KY7A 2V3KA 2I6DA 5GMBA 1X7OA 4YQ9A 1K3RA 2OZ9R 1Z85A 4YQTA 4FMWA 3KORA 2Z0YA 4YQ8A 1TO0A 3IC6A 3KW2A 3OIJA 1UALA 5D9FA 2EGVA 5GMCA 2XDIA 4YQSA 4YQLA 2HA8A 3KNUA 1TROA 4MCBA 1UAKA 2EGWA 4YVGA 4MCDA 3NK7A 1IPAA 1GZ0A 1UAJA 3O7BA 4YQ3A 4YVIA 3SSWN 3KTYA 4CNFA 4XBOA 4YPZA 3AIAA 4JALA 4YQBA 3OINA 4X3MA 2QWVA 4YQQA 1V6ZA 4L69A 4CNDA 4JAKA 4YQAA 2O3AA 3DCMX 4IG6A 4JWFA 3QUVA 3SSXN 4X3LA 1ZT9A 1X7PA 4YVKA 4YPWA 3L8UA 4YQ0A 4YQ6A 1UAMA 4JWJA 4YQCA 2CX8A 4CNEA 5CO4A 1VH0A 4J3CA 4JWGA 4PZKA 4YQDA 4YQ4A 4YVJA 3AI9X 1RCSA 4YQGA 1O6DA 1V2XA 2V3JA 1VHKA 4FAKA 4YQPA 1NXZA 4CNGA 4H3ZA 4YVHA 1NS5A 2QMMA 1VHYA 3N4KA 1MI7R 3BBEA 5GM8A 4YQNA 5FAIA 4YQRA 4YPYA 4YPXA 1WRPR 4H3YA 1TRRA 3NK6A 3G1CA 3BBHA 3E5YA 1J85A 4YQIA 4YQJA 1JHGA 1WRTR 3ILKA 1CO0A 4JWHA 4YQ2A 1P9PA
chains in the Genus database with same CATH topology
4YQ1A 4RG1A 4YQOA 3N4JA 4YQ7A 4MCCA 4KGNA 1MXIA 1OY5A 4KDZA 4E8BA 4YQ5A 3ONPA 2YY8A 3IEFA 3OIIA 3BBDA 4YQKA 1ZJRA 3GYQA 3AXZA 3KY7A 2V3KA 2I6DA 5GMBA 1X7OA 4YQ9A 1Z85A 1K3RA 4YQTA 4FMWA 2Z0YA 4YQ8A 1TO0A 3IC6A 3KW2A 3OIJA 1UALA 5D9FA 2EGVA 5GMCA 4YQSA 4YQLA 2HA8A 3KNUA 4MCBA 1UAKA 2EGWA 4YVGA 4MCDA 3NK7A 1IPAA 1GZ0A 1UAJA 3O7BA 4YQ3A 4YVIA 3KTYA 4CNFA 4XBOA 4YPZA 3AIAA 4JALA 4YQBA 3OINA 4X3MA 2QWVA 4YQQA 1V6ZA 4L69A 4CNDA 4JAKA 4YQAA 2O3AA 3DCMX 4IG6A 4JWFA 3QUVA 4X3LA 1X7PA 4YVKA 4YPWA 3L8UA 4YQ0A 4YQ6A 1UAMA 4JWJA 4YQCA 2CX8A 4CNEA 5CO4A 1VH0A 4J3CA 4JWGA 4PZKA 4YQDA 4YQ4A 4YVJA 3AI9X 1O6DA 4YQGA 1V2XA 2V3JA 1VHKA 4FAKA 4YQPA 1NXZA 4CNGA 4YVHA 4H3ZA 1NS5A 2QMMA 1VHYA 3N4KA 5GM8A 3BBEA 4YQNA 5FAIA 4YQRA 4YPYA 4YPXA 3NK6A 4H3YA 3BBHA 3E5YA 1J85A 4YQIA 4YQJA 3ILKA 4JWHA 4YQ2A 1P9PA
chains in the Genus database with same CATH homology


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