4YVJA

Crystal structure of h. influenzae trmd in complex with sinefungin and trna variant (g36u)
Knot K +31
Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
+31 89-132 44 1-88, 133-248 88 116 knot
Chain Sequence
SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGV---------DSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
Whole chain analysis
Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1

Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
3.1 88-133 46 1-87, 134-239 87 106 knot
view details
2.1 85-130 46 1-84 136-239 131-135 84 104 slipknot
view details
2.1 90-200 111 1-87, 209-239 88-89, 201-208 87 31 slipknot
view details
2.1 90-208 119 1-87, 211-239 88-89, 209-210 87 29 slipknot
view details
2.1 90-210 121 211-239 1-87 88-89 87 28 slipknot
missing residues 162-170
publication title Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
pubmed doi rcsb
structure length 239
molecule tags Transferase/rna
source organism Haemophilus influenzae (strain atcc 51907 / dsm 11121 / kw20 / rd)
sequence length 248
molecule keywords tRNA (guanine-N(1)-)-methyltransferase
ec nomenclature ec 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
pdb deposition date 2015-03-20
KnotProt deposition date 2015-12-25

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)
4YQDA 4YVGA 4YQTA 4MCDA 4YVHA 4YQRA 3QUVA 1UALA 4YQSA 4YPXA 1UAJA 4MCBA 4MCCA 1UAKA 4H3ZA 3AXZA 5WYQA 4IG6A 3KNUA 1UAMA 4H3YA 5WYRA 3KY7A 3IEFA 1P9PA 4YVJA 4YVKA 4YVIA 1OY5A
similar chains in the KnotProt database (40% sequence similarity)
4YQAA 4YQ9A 3QUVB 4YQOA 4YQ5A 4YQ0A 4YQQA 4YQKA 4YQ7A 4YPZA 4YQCA 4YQGA 4YPYA 4YQ4A 4YQJA 4YQIA 4YQ8A 4YQ6A 4MCBB 5D9FA 4MCCB 4YQ1A 4YQBA 4H3ZB 4YQNA 5WYQB 3KNUB 3KNUC 3KNUD 4YPWA 4YQ3A 4YQLA 4H3YB 5WYRB 4YQPA 3IEFB 4YQ2A 4YVJB 4YVKB 4YVIB 1OY5B 1OY5C
similar chains in the pdb database (40% sequence similarity)

 
            
               
#similar chains in the KnotProt database (40% sequence similarity)
 4YQD A;  4YVG A;  4YQT A;  4MCD A;  4YVH A;  4YQR A;  3QUV A;  1UAL A;  4YQS A;  4YPX A;  1UAJ A;  4MCB A;  4MCC A;  1UAK A;  4H3Z A;  3AXZ A;  5WYQ A;  4IG6 A;  3KNU A;  1UAM A;  4H3Y A;  5WYR A;  3KY7 A;  3IEF A;  1P9P A;  4YVJ A;  4YVK A;  4YVI A; 
               
               
#similar chains, but unknotted
 1OY5 A;                               
               
           
#similar chains in the pdb database (40% sequence similarity)
 4YQA A;  4YQ9 A;  3QUV B;  4YQO A;  4YQ5 A;  4YQ0 A;  4YQQ A;  4YQK A;  4YQ7 A;  4YPZ A;  4YQC A;  4YQG A;  4YPY A;  4YQ4 A;  4YQJ A;  4YQI A;  4YQ8 A;  4YQ6 A;  4MCB B;  5D9F A;  4MCC B;  4YQ1 A;  4YQB A;  4H3Z B;  4YQN A;  5WYQ B;  3KNU B;  3KNU C;  3KNU D;  4YPW A;  4YQ3 A;  4YQL A;  4H3Y B;  5WYR B;  4YQP A;  3IEF B;  4YQ2 A;  4YVJ B;  4YVK B;  4YVI B;  1OY5 B;  1OY5 C; 
           

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