2I6DA

The structure of a putative rna methyltransferase of the trmh family from porphyromonas gingivalis.
Warning
  • Chain breaks within knot 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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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: 73
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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+31 179-221 43 1-178, 222-255 178 34 knot
Chain Sequence
AMLSANQIKFLRSLRERKYRLREQAFAVEGPKLVGEMLPFYRCRMLVGTAAMLRAVSTPHDAEVVELPESFDFKRISTQTTPQPLMAVFDLPAEPEPVVEGLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASMGALARVQPTPLKNTVDTLAYFRRQGIPVYGAFLDGQSLYEAPLPNFTEPAILVLGSEGRGISPEVAAEITDRLTIPASGLSV----ESLNVAIATAILCSEWRRRS
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
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3.1 178-224 47 1-177, 225-251 177 27 knot
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2.1 178-218 41 1-177 225-251 219-224 177 27 slipknot
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3.1 179-224 46 225-251 1-177 178-178 177 26 slipknot
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3.1 181-234 54 1-178, 242-251 179-180, 235-241 178 10 slipknot
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3.1 180-242 63 243-251 1-178 179-179 178 8 slipknot
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3.1 181-243 63 1-179, 251-251 180-180, 244-250 179 1 slipknot
sequence length 255
structure length 251
publication title The structure of a putative RNA methyltransferase of the TrmH family from Porphyromonas gingivalis.
rcsb
molecule tags Transferase
molecule keywords RNA methyltransferase, TrmH family
source organism Porphyromonas gingivalis
missing residues 232-235
total genus Genus: 73
ec nomenclature ec 2.1.1.-:
pdb deposition date 2006-08-28
KnotProt deposition date 2014-07-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00588 SpoU_methylase SpoU rRNA Methylase family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.30.1330.30 Alpha Beta 2-Layer Sandwich 60s Ribosomal Protein L30; Chain: A; 60s Ribosomal Protein L30; Chain: A; 2i6dA01
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 2i6dA02
3IC6A 1X7OA 1V6ZA 4FAKA 4IG6A 1O6DA 2I6DA 1VH0A 3AXZA 2QWVA 1J85A 2QMMA 3ILKA 2CX8A 2YY8A 3QUVA 3E5YA 1X7PA 3NK7A 1UAJA 3L8UA 3N4KA 1NS5A 1VHKA 1V2XA 3AIAA 4CNFB 3AI9X 2Z0YA 1UALA 3DCMX 1NXZA 3ONPA 4H3YA 1GZ0A 3GYQA 1VHYA 1ZJRA 3KTYA 4CNGB 1TO0A 2HA8A 1UAKA 3KY7A 1K3RA 3KNUA 3NK6A 2O3AA 1MXIA 3N4JA 4CNEB 3IEFA 4H3ZA 1UAMA 1P9PA 4E8BA
chains in the KnotProt database with same CATH superfamily
3IC6A 1X7OA 1V6ZA 4FAKA 4IG6A 1O6DA 2I6DA 1VH0A 3AXZA 2QWVA 1J85A 2QMMA 3ILKA 2CX8A 2YY8A 3QUVA 3E5YA 1X7PA 3NK7A 1UAJA 3L8UA 3N4KA 1NS5A 1VHKA 1V2XA 3AIAA 4CNFB 3AI9X 2Z0YA 1UALA 3DCMX 1NXZA 3ONPA 4H3YA 1GZ0A 3GYQA 1VHYA 1ZJRA 3KTYA 4CNGB 1TO0A 2HA8A 1UAKA 3KY7A 1K3RA 3KNUA 3NK6A 2O3AA 1MXIA 3N4JA 4CNEB 3IEFA 4H3ZA 1UAMA 1P9PA 4E8BA
chains in the KnotProt database with same CATH topology
3IC6A 1X7OA 1V6ZA 4FAKA 4IG6A 1O6DA 2I6DA 1VH0A 3AXZA 2QWVA 1J85A 2QMMA 3ILKA 2CX8A 2YY8A 3QUVA 3E5YA 1X7PA 3NK7A 1UAJA 3L8UA 3N4KA 1NS5A 1VHKA 1V2XA 3AIAA 4CNFB 3AI9X 2Z0YA 1UALA 3DCMX 1NXZA 3ONPA 4H3YA 1GZ0A 3GYQA 1VHYA 1ZJRA 3KTYA 4CNGB 1TO0A 2HA8A 1UAKA 3KY7A 1K3RA 3KNUA 3NK6A 2O3AA 1MXIA 3N4JA 4CNEB 3IEFA 4H3ZA 1UAMA 1P9PA 4E8BA
chains in the KnotProt database with same CATH homology

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