1K3RA

Crystal structure of the methyltransferase with a knot from methanobacterium thermoautotrophicum
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
+31 187-232 46 1-186, 233-262 186 30 knot
Chain Sequence
MNRVDLSLFIPDSLTAETGDLKIKTYKVVLIARAASIFGVKRIVIYHDDADGEARFIRDILTYMDTPQYLRRKVFPIMRELKHVGILPPLRTPHHPTGKPVTGEYRQGLTVKRVKKGTLVDIGADKLALCREKLTVNRIMSFRVVRLGKEILIEPDEPEDRYWGYEVLDTRRNLAESLKTVGADVVVATSRNASPITSILDEVKTRMRGAREAAILFGGPYKGLPEIDADIWVNTLPGQCTETVRTEEAVLATLSVFNMLTQ
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
3.1 187-234 48 1-186, 235-262 186 28 knot
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2.1 186-229 44 1-185 236-262 230-235 185 27 slipknot
view details
2.1 189-242 54 1-186, 255-262 187-188, 243-254 186 8 slipknot
view details
3.1 189-239 51 1-186, 243-262 187-188, 240-242 186 20 slipknot
publication title Deep trefoil knot implicated in RNA binding found in an archaebacterial protein.
pubmed doi rcsb
structure length 262
molecule tags Structural genomics, unknown function
source organism Methanothermobacter thermautotrophicus
sequence length 262
total genus Genus: 73
molecule keywords conserved protein MT0001
ec nomenclature
pdb deposition date 2001-10-03
KnotProt deposition date 2014-07-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF02598 Methyltrn_RNA_3 Putative RNA methyltransferase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.40.50.140 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins 1k3rA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 1k3rA01
3KTYA 1K3RA 3E5YA 1VHKA 1UALA 1GZ0A 3IEFA 3AI9X 3KNUA 1UAJA 1ZJRA 3NK6A 2QMMA 2HA8A 3KY7A 1X7OA 1J85A 1NS5A 3IC6A 3NK7A 3ONPA 3AXZA 3GYQA 1NXZA 2Z0YA 3L8UA 4E8BA 3ILKA 3DCMX 3N4KA 4IG6A 1VHYA 2CX8A 3N4JA 3AIAA 1MXIA 4H3ZA 2I6DA 1X7PA 2O3AA 1P9PA 2YY8A 3QUVA 1V6ZA 4FAKA 1TO0A 1O6DA 2QWVA 1V2XA 1UAMA 4H3YA 1VH0A 1IPAA 1UAKA
chains in the KnotProt database with same CATH superfamily
3KTYA 1K3RA 3E5YA 1VHKA 1UALA 1GZ0A 3IEFA 3AI9X 3KNUA 1UAJA 1ZJRA 3NK6A 1TWHB 2QMMA 2HA8A 3KY7A 1X7OA 1J85A 1NS5A 3IC6A 3NK7A 3ONPA 3AXZA 3GYQA 1NXZA 2Z0YA 1TWGB 4E8BA 3ILKA 3DCMX 3N4KA 4IG6A 1VHYA 2CX8A 3N4JA 3AIAA 1MXIA 4H3ZA 3L8UA 2I6DA 1X7PA 2O3AA 1P9PA 2YY8A 3QUVA 1V6ZA 4FAKA 1TO0A 1O6DA 2QWVA 1V2XA 1UAMA 4H3YA 1VH0A 1IPAA 1UAKA
chains in the KnotProt database with same CATH topology
3KTYA 1K3RA 3E5YA 1VHKA 1UALA 1GZ0A 3IEFA 3AI9X 3KNUA 1UAJA 1ZJRA 3NK6A 2QMMA 2HA8A 3KY7A 1X7OA 1J85A 1NS5A 3IC6A 3NK7A 3ONPA 3AXZA 3GYQA 1NXZA 2Z0YA 3L8UA 4E8BA 3ILKA 3DCMX 3N4KA 4IG6A 1VHYA 2CX8A 3N4JA 3AIAA 1MXIA 4H3ZA 2I6DA 1X7PA 2O3AA 1P9PA 2YY8A 3QUVA 1V6ZA 4FAKA 1TO0A 1O6DA 2QWVA 1V2XA 1UAMA 4H3YA 1VH0A 1IPAA 1UAKA
chains in the KnotProt database with same CATH homology


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