4YQRA

Crystal structure of trmd, a m1g37 trna methyltransferase with sam-competitive compounds
Total Genus 74
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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
74
Knots found
sequence length
248
structure length
240
Chain Sequence
SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
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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 tags Transferase/transferase inhibitor
source organism Haemophilus influenzae (strain atcc 51907 / dsm 11121 / kw20 / rd)
publication title Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
rcsb
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 2015-03-13

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 4yqrA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4yqrA01
3DCMX 4YPZA 3AI9X 3E5YA 1V2XA 4X3LA 3NK6A 1O6DA 3BBDA 4E8BA 5GMCA 4YPYA 4YQRA 1VHYA 4J3CA 3KNUA 4YQAA 4YQQA 1TO0A 4YQ5A 1IPAA 3O7BA 3OIJA 1UAKA 1VH0A 3BBEA 3IEFA 4KGNA 4YQOA 4YQJA 4YQ7A 1P9PA 2CX8A 4YQ1A 4MCBA 4H3ZA 4RG1A 1V6ZA 3GYQA 3ONPA 4JAKA 4YQCA 2V3JA 3N4KA 3NK7A 4YVHA 3IC6A 2QWVA 4YQLA 4FAKA 1Z85A 1UALA 4YQ4A 5CO4A 4MCDA 1OY5A 4YQGA 4CNFA 3BBHA 4YVKA 1X7OA 1GZ0A 3KTYA 3QUVA 2O3AA 3ILKA 4CNEA 4YQ8A 2QMMA 4YQSA 3AXZA 3OIIA 4X3MA 4YQPA 4YQTA 4CNGA 4YVIA 4PZKA 5D9FA 4YPXA 2V3KA 4JALA 4YQ6A 4YVJA 4YQKA 4L69A 3OINA 1VHKA 4YQNA 4YPWA 2I6DA 2YY8A 3L8UA 4YQ3A 1X7PA 2EGWA 5GMBA 4YQBA 1MXIA 4IG6A 3N4JA 2Z0YA 2HA8A 4YQDA 1NS5A 3KW2A 1J85A 1UAJA 1ZJRA 4YQ2A 2EGVA 5FAIA 4YQ0A 4KDZA 4MCCA 4YQ9A 3KY7A 4XBOA 1UAMA 4H3YA 4CNDA 1K3RA 4YQIA 3AIAA 1NXZA 4YVGA 5GM8A
chains in the Genus database with same CATH superfamily
3DCMX 1TRRA 4YPZA 3AI9X 3WRPA 3E5YA 1V2XA 4X3LA 3NK6A 1O6DA 3BBDA 4E8BA 5GMCA 4YPYA 3G1CA 4YQRA 1VHYA 4J3CA 3KNUA 4YQAA 4YQQA 1TO0A 4YQ5A 1IPAA 3O7BA 3OIJA 1UAKA 1VH0A 3BBEA 3IEFA 4KGNA 4JWGA 4YQOA 3SSWN 4YQJA 4YQ7A 1P9PA 2CX8A 4YQ1A 4MCBA 4H3ZA 4RG1A 1V6ZA 3GYQA 3ONPA 4JAKA 4YQCA 2V3JA 1ZT9A 3N4KA 3NK7A 4YVHA 3IC6A 2QWVA 4YQLA 4FAKA 1Z85A 4JWFA 3KORA 1UALA 4YQ4A 1WRSR 5CO4A 4MCDA 1OY5A 4YQGA 4CNFA 3FRWA 3BBHA 4YVKA 1X7OA 4JWJA 1GZ0A 3KTYA 3QUVA 2O3AA 1WRTR 3ILKA 4FMWA 4YQ8A 2QMMA 4YQSA 3AXZA 3OIIA 4CNEA 4X3MA 4YQPA 4YQTA 1RCSA 4CNGA 4YVIA 2XDIA 4PZKA 5D9FA 4YPXA 2V3KA 2OZ9R 4JALA 4YQ6A 4YVJA 4YQKA 4L69A 3OINA 1VHKA 4YQNA 4YPWA 2I6DA 2YY8A 3L8UA 4YQ3A 1X7PA 2EGWA 5GMBA 4YQBA 1MXIA 4IG6A 3N4JA 4JWHA 2Z0YA 2HA8A 4YQDA 1JHGA 1NS5A 3KW2A 1J85A 1UAJA 1ZJRA 4YQ2A 2EGVA 1CO0A 4YQ0A 5FAIA 4KDZA 4MCCA 1WRPR 4YQ9A 3KY7A 4XBOA 1UAMA 1MI7R 4H3YA 3SSXN 4CNDA 1K3RA 4YQIA 3AIAA 1TROA 1NXZA 4YVGA 5GM8A
chains in the Genus database with same CATH topology
3DCMX 4YPZA 3AI9X 3E5YA 1V2XA 4X3LA 3NK6A 1O6DA 3BBDA 4E8BA 5GMCA 4YPYA 4YQRA 1VHYA 4J3CA 3KNUA 4YQAA 4YQQA 1TO0A 4YQ5A 1IPAA 3O7BA 3OIJA 1UAKA 1VH0A 3BBEA 3IEFA 4KGNA 4JWGA 4YQOA 4YQJA 4YQ7A 1P9PA 2CX8A 4YQ1A 4MCBA 4H3ZA 4RG1A 1V6ZA 3GYQA 3ONPA 4JAKA 4YQCA 2V3JA 3N4KA 3NK7A 4YVHA 3IC6A 2QWVA 4YQLA 4FAKA 1Z85A 4JWFA 1UALA 4YQ4A 5CO4A 4MCDA 1OY5A 4YQGA 4CNFA 3BBHA 4YVKA 1X7OA 4JWJA 1GZ0A 3KTYA 3QUVA 2O3AA 3ILKA 4FMWA 4YQ8A 2QMMA 4YQSA 3AXZA 3OIIA 4CNEA 4X3MA 4YQPA 4YQTA 4CNGA 4YVIA 4PZKA 5D9FA 4YPXA 2V3KA 4JALA 4YQ6A 4YVJA 4YQKA 4L69A 3OINA 1VHKA 4YQNA 4YPWA 2I6DA 2YY8A 3L8UA 4YQ3A 1X7PA 2EGWA 5GMBA 4YQBA 1MXIA 4IG6A 3N4JA 4JWHA 2Z0YA 2HA8A 4YQDA 1NS5A 3KW2A 1J85A 1UAJA 1ZJRA 4YQ2A 2EGVA 5FAIA 4YQ0A 4KDZA 4MCCA 4YQ9A 3KY7A 4XBOA 1UAMA 4H3YA 4CNDA 1K3RA 4YQIA 3AIAA 1NXZA 4YVGA 5GM8A
chains in the Genus database with same CATH homology


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