2I6DA

The structure of a putative rna methyltransferase of the trmh family from porphyromonas gingivalis.
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
4CNEB 3AIAA 3N4JA 2HA8A 1V2XA 1TO0A 3ONPA 1UAJA 1VHYA 3N4KA 1V6ZA 3GYQA 4CNGB 2O3AA 3IEFA 1UAKA 1MXIA 3ILKA 3L8UA 1O6DA 1X7OA 1NXZA 3DCMX 2QMMA 2CX8A 4H3YA 3KY7A 4IG6A 1UALA 1VHKA 3NK7A 2Z0YA 1J85A 2YY8A 1K3RA 1VH0A 4FAKA 1UAMA 3QUVA 1NS5A 1X7PA 3AI9X 3NK6A 4CNFB 4E8BA 3IC6A 1ZJRA 3E5YA 1GZ0A 3KTYA 3KNUA 3AXZA 2QWVA 1P9PA 4H3ZA 2I6DA
chains in the KnotProt database with same CATH superfamily
4CNEB 3AIAA 3N4JA 2HA8A 1V2XA 1TO0A 3ONPA 1UAJA 1VHYA 3N4KA 1V6ZA 3GYQA 4CNGB 2O3AA 3IEFA 1UAKA 1MXIA 3ILKA 3L8UA 1O6DA 1X7OA 1NXZA 3DCMX 2QMMA 2CX8A 4H3YA 3KY7A 4IG6A 1UALA 1VHKA 3NK7A 2Z0YA 1J85A 2YY8A 1K3RA 1VH0A 4FAKA 1UAMA 3QUVA 1NS5A 1X7PA 3AI9X 3NK6A 4CNFB 4E8BA 3IC6A 1ZJRA 3E5YA 1GZ0A 3KTYA 3KNUA 3AXZA 2QWVA 1P9PA 4H3ZA 2I6DA
chains in the KnotProt database with same CATH topology
4CNEB 3AIAA 3N4JA 2HA8A 1V2XA 1TO0A 3ONPA 1UAJA 1VHYA 3N4KA 1V6ZA 3GYQA 4CNGB 2O3AA 3IEFA 1UAKA 1MXIA 3ILKA 3L8UA 1O6DA 1X7OA 1NXZA 3DCMX 2QMMA 2CX8A 4H3YA 3KY7A 4IG6A 1UALA 1VHKA 3NK7A 2Z0YA 1J85A 2YY8A 1K3RA 1VH0A 4FAKA 1UAMA 3QUVA 1NS5A 1X7PA 3AI9X 3NK6A 4CNFB 4E8BA 3IC6A 1ZJRA 3E5YA 1GZ0A 3KTYA 3KNUA 3AXZA 2QWVA 1P9PA 4H3ZA 2I6DA
chains in the KnotProt database with same CATH homology

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