4YPXA

Crystal structure of trmd, a m1g37 trna methyltransferase with sam-competitive compounds
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
249
structure length
239
Chain Sequence
RGSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHN
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/transferase inhibitor
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)
total genus 74
structure length 239
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 4ypxA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4ypxA01
4JAKA 4KDZA 4YQOA 4YPZA 3DCMX 3N4JA 5GMCA 1GZ0A 4YQDA 4JALA 5CO4A 1Z85A 3OIJA 5GMBA 4L69A 3KNUA 4YQ5A 4E8BA 1MXIA 4YPWA 3GYQA 1NXZA 1V2XA 4YVJA 2EGWA 4YQSA 3O7BA 2QMMA 4X3MA 1J85A 4YQQA 3OIIA 3IC6A 4YQ4A 4YQGA 4FAKA 4YQRA 3NK7A 4J3CA 4YVGA 3ILKA 4YPXA 3N4KA 5GM8A 3L8UA 3BBDA 2YY8A 3BBEA 2V3JA 1NS5A 4YQCA 1K3RA 4YVIA 2HA8A 4YQ1A 1OY5A 2V3KA 5FAIA 2O3AA 3NK6A 1UAKA 3AI9X 4YQTA 3IEFA 1ZJRA 4YQNA 4YQAA 4CNFA 2CX8A 4YQ2A 4MCDA 4IG6A 4CNDA 1VH0A 4PZKA 1TO0A 3QUVA 1X7OA 2QWVA 2EGVA 1VHKA 4CNEA 3OINA 1VHYA 4CNGA 2Z0YA 1X7PA 4YPYA 4YQIA 4MCBA 4YQKA 3KY7A 1P9PA 1UALA 3BBHA 4YQ6A 2I6DA 1IPAA 4YVHA 1UAJA 3KW2A 4YQ8A 5D9FA 4YVKA 1O6DA 4RG1A 4YQ9A 4KGNA 4X3LA 4YQ7A 4YQPA 3E5YA 3AIAA 1V6ZA 4YQLA 4H3ZA 4MCCA 4YQ3A 4XBOA 3ONPA 1UAMA 4YQBA 3AXZA 4H3YA 4YQ0A 3KTYA 4YQJA
chains in the Genus database with same CATH superfamily
4JAKA 3KORA 4KDZA 3SSWN 4YQOA 4YPZA 3DCMX 3N4JA 5GMCA 1GZ0A 4YQDA 1WRSR 4JALA 5CO4A 1Z85A 3OIJA 5GMBA 4JWFA 4L69A 3KNUA 4YQ5A 4E8BA 1MXIA 4YPWA 3GYQA 1NXZA 1V2XA 4YVJA 2EGWA 1TRRA 4YQSA 3O7BA 2QMMA 4X3MA 1J85A 4YQQA 3OIIA 1MI7R 3IC6A 4YQ4A 4YQGA 4FAKA 2OZ9R 4YQRA 3NK7A 1ZT9A 4J3CA 4YVGA 3ILKA 4JWGA 4YPXA 3N4KA 1RCSA 5GM8A 3L8UA 3BBDA 1CO0A 2YY8A 4FMWA 3BBEA 2V3JA 1NS5A 4YQCA 1K3RA 4YVIA 2HA8A 4YQ1A 1OY5A 2V3KA 5FAIA 2O3AA 4JWHA 3NK6A 1UAKA 3AI9X 4YQTA 3IEFA 1ZJRA 4YQNA 4YQAA 4CNFA 2CX8A 1WRPR 1JHGA 4YQ2A 4MCDA 3SSXN 4IG6A 4JWJA 4CNDA 1TROA 1VH0A 4PZKA 1TO0A 3QUVA 1X7OA 2QWVA 2EGVA 1VHKA 4CNEA 3OINA 2XDIA 1VHYA 4CNGA 2Z0YA 4YPYA 4YQIA 1X7PA 4MCBA 4YQKA 3KY7A 1P9PA 1UALA 3BBHA 3WRPA 4YQ6A 2I6DA 1IPAA 1WRTR 4YVHA 1UAJA 3KW2A 4YQ8A 5D9FA 3FRWA 4YVKA 1O6DA 4RG1A 4YQ9A 4KGNA 4X3LA 4YQ7A 4YQPA 3E5YA 3AIAA 1V6ZA 4YQLA 4H3ZA 4MCCA 4YQ3A 3G1CA 4XBOA 3ONPA 1UAMA 4YQBA 3AXZA 4H3YA 4YQ0A 3KTYA 4YQJA
chains in the Genus database with same CATH topology
4JAKA 4KDZA 4YQOA 4YPZA 3DCMX 3N4JA 5GMCA 1GZ0A 4YQDA 4JALA 5CO4A 1Z85A 3OIJA 5GMBA 4JWFA 4L69A 3KNUA 4YQ5A 4E8BA 1MXIA 4YPWA 3GYQA 1NXZA 1V2XA 4YVJA 2EGWA 4YQSA 3O7BA 2QMMA 4X3MA 1J85A 4YQQA 3OIIA 3IC6A 4YQ4A 4YQGA 4FAKA 4YQRA 3NK7A 4J3CA 4YVGA 3ILKA 4JWGA 4YPXA 3N4KA 5GM8A 3L8UA 3BBDA 2YY8A 4FMWA 3BBEA 2V3JA 1NS5A 4YQCA 1K3RA 4YVIA 2HA8A 4YQ1A 1OY5A 2V3KA 5FAIA 2O3AA 4JWHA 3NK6A 1UAKA 3AI9X 4YQTA 3IEFA 1ZJRA 4YQNA 4YQAA 4CNFA 2CX8A 4YQ2A 4MCDA 4IG6A 4JWJA 4CNDA 1VH0A 4PZKA 1TO0A 3QUVA 1X7OA 2QWVA 2EGVA 1VHKA 4CNEA 3OINA 1VHYA 4CNGA 2Z0YA 1X7PA 4YPYA 4YQIA 4MCBA 4YQKA 3KY7A 1P9PA 1UALA 3BBHA 4YQ6A 2I6DA 1IPAA 4YVHA 1UAJA 3KW2A 4YQ8A 5D9FA 4YVKA 1O6DA 4RG1A 4YQ9A 4KGNA 4X3LA 4YQ7A 4YQPA 3E5YA 3AIAA 1V6ZA 4YQLA 4H3ZA 4MCCA 4YQ3A 4XBOA 3ONPA 1UAMA 4YQBA 3AXZA 4H3YA 4YQ0A 3KTYA 4YQJA
chains in the Genus database with same CATH homology


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