4H3ZA

Crystal structure of a symmetric dimer of a trna (guanine-(n(1)-)-methyltransferase from burkholderia phymatum bound to s-adenosyl homocystein in both half-sites
Warning
  • Chain breaks within knotoid 31 (displayed as a gray area on the plot and as '-' on the sequence). The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Genus: 81
Knot K +31

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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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+31 92-135 44 1-91, 136-255 91 120 knot
Chain Sequence
SMQFDIVTLFPDMFRALTDWGITSRAAKQERYGLRTWNPRDFTTDNYRTIDDRPYGGGPGMVMLARPLEDAINAAKAAQAEQGIGGARVVMMSPQGATLNHDKVMRFAAEPGLILLCGRYEAIDQRLIDRVVDEEVSLGDFVLSGGELPAMALIDAVVRHLPGVLN------QDSFVDGLLDCPHYTRPEEYDGVRVPDVLLGGHHAEIEQWRRREALRNTWLKRPDLIVQARKNKLLSRADEAWLASLAKDASK
Whole chain analysis

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Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1


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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 91-136 46 1-90, 137-249 90 113 knot
sequence length 255
structure length 249
publication title Combining functional and structural genomics to sample the essential Burkholderia structome.
pubmed doi rcsb
molecule tags Transferase
molecule keywords tRNA (guanine-N(1)-)-methyltransferase
source organism Burkholderia phymatum
missing residues 167-172
total genus Genus: 81
ec nomenclature ec 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
pdb deposition date 2012-09-14
KnotProt deposition date 2014-07-31

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 4h3zA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4h3zA01
4H3YA 3KY7A 2O3AA 3L8UA 3N4JA 1NS5A 1NXZA 1MXIA 3IEFA 1V2XA 3KTYA 2HA8A 4E8BA 4IG6A 1O6DA 2Z0YA 1UAKA 2YY8A 1J85A 3ILKA 1GZ0A 1VH0A 3KNUA 1V6ZA 4CNEB 1UALA 1P9PA 1UAJA 1X7OA 2I6DA 2QWVA 3N4KA 3NK7A 1ZJRA 3E5YA 1X7PA 3NK6A 1K3RA 1VHYA 3AI9X 4H3ZA 2QMMA 4CNGB 4CNFB 3DCMX 3GYQA 3IC6A 3ONPA 3QUVA 2CX8A 4FAKA 3AIAA 1TO0A 1VHKA 1UAMA 3AXZA
chains in the KnotProt database with same CATH superfamily
4H3YA 3KY7A 2O3AA 3L8UA 3N4JA 1NS5A 1NXZA 1MXIA 3IEFA 1V2XA 3KTYA 2HA8A 4E8BA 4IG6A 1O6DA 2Z0YA 1UAKA 2YY8A 1J85A 3ILKA 1GZ0A 1VH0A 3KNUA 1V6ZA 4CNEB 1UALA 1P9PA 1UAJA 1X7OA 2I6DA 2QWVA 3N4KA 3NK7A 1ZJRA 3E5YA 1X7PA 3NK6A 1K3RA 1VHYA 3AI9X 4H3ZA 2QMMA 4CNGB 4CNFB 3DCMX 3GYQA 3IC6A 3ONPA 3QUVA 2CX8A 4FAKA 3AIAA 1TO0A 1VHKA 1UAMA 3AXZA
chains in the KnotProt database with same CATH topology
4H3YA 3KY7A 2O3AA 3L8UA 3N4JA 1NS5A 1NXZA 1MXIA 3IEFA 1V2XA 3KTYA 2HA8A 4E8BA 4IG6A 1O6DA 2Z0YA 1UAKA 2YY8A 1J85A 3ILKA 1GZ0A 1VH0A 3KNUA 1V6ZA 4CNEB 1UALA 1P9PA 1UAJA 1X7OA 2I6DA 2QWVA 3N4KA 3NK7A 1ZJRA 3E5YA 1X7PA 3NK6A 1K3RA 1VHYA 3AI9X 4H3ZA 2QMMA 4CNGB 4CNFB 3DCMX 3GYQA 3IC6A 3ONPA 3QUVA 2CX8A 4FAKA 3AIAA 1TO0A 1VHKA 1UAMA 3AXZA
chains in the KnotProt database with same CATH homology

  
#chains in the KnotProt database with same CATH superfamily
 4H3Y A;  3KY7 A;  2O3A A;  3L8U A;  3N4J A;  1NS5 A;  1NXZ A;  1MXI A;  3IEF A;  1V2X A;  3KTY A;  2HA8 A;  4E8B A;  4IG6 A;  1O6D A;  2Z0Y A;  1UAK A;  2YY8 A;  1J85 A;  3ILK A;  1GZ0 A;  1VH0 A;  3KNU A;  1V6Z A;  4CNE B;  1UAL A;  1P9P A;  1UAJ A;  1X7O A;  2I6D A;  2QWV A;  3N4K A;  3NK7 A;  1ZJR A;  3E5Y A;  1X7P A;  3NK6 A;  1K3R A;  1VHY A;  3AI9 X;  4H3Z A;  2QMM A;  4CNG B;  4CNF B;  3DCM X;  3GYQ A;  3IC6 A;  3ONP A;  3QUV A;  2CX8 A;  4FAK A;  3AIA A;  1TO0 A;  1VHK A;  1UAM A;  3AXZ A; 
#chains in the KnotProt database with same CATH topology
 4H3Y A;  3KY7 A;  2O3A A;  3L8U A;  3N4J A;  1NS5 A;  1NXZ A;  1MXI A;  3IEF A;  1V2X A;  3KTY A;  2HA8 A;  4E8B A;  4IG6 A;  1O6D A;  2Z0Y A;  1UAK A;  2YY8 A;  1J85 A;  3ILK A;  1GZ0 A;  1VH0 A;  3KNU A;  1V6Z A;  4CNE B;  1UAL A;  1P9P A;  1UAJ A;  1X7O A;  2I6D A;  2QWV A;  3N4K A;  3NK7 A;  1ZJR A;  3E5Y A;  1X7P A;  3NK6 A;  1K3R A;  1VHY A;  3AI9 X;  4H3Z A;  2QMM A;  4CNG B;  4CNF B;  3DCM X;  3GYQ A;  3IC6 A;  3ONP A;  3QUV A;  2CX8 A;  4FAK A;  3AIA A;  1TO0 A;  1VHK A;  1UAM A;  3AXZ A; 
#chains in the KnotProt database with same CATH homology
 4H3Y A;  3KY7 A;  2O3A A;  3L8U A;  3N4J A;  1NS5 A;  1NXZ A;  1MXI A;  3IEF A;  1V2X A;  3KTY A;  2HA8 A;  4E8B A;  4IG6 A;  1O6D A;  2Z0Y A;  1UAK A;  2YY8 A;  1J85 A;  3ILK A;  1GZ0 A;  1VH0 A;  3KNU A;  1V6Z A;  4CNE B;  1UAL A;  1P9P A;  1UAJ A;  1X7O A;  2I6D A;  2QWV A;  3N4K A;  3NK7 A;  1ZJR A;  3E5Y A;  1X7P A;  3NK6 A;  1K3R A;  1VHY A;  3AI9 X;  4H3Z A;  2QMM A;  4CNG B;  4CNF B;  3DCM X;  3GYQ A;  3IC6 A;  3ONP A;  3QUV A;  2CX8 A;  4FAK A;  3AIA A;  1TO0 A;  1VHK A;  1UAM A;  3AXZ A;
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similar chains in the KnotProt database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

  
#similar chains in the KnotProt database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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How to cite
KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling