2I6DA

The structure of a putative rna methyltransferase of the trmh family from porphyromonas gingivalis.
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
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+31 179-221 43 1-178, 222-255 178 34 knot
Chain Sequence
AMLSANQIKFLRSLRERKYRLREQAFAVEGPKLVGEMLPFYRCRMLVGTAAMLRAVSTPHDAEVVELPESFDFKRISTQTTPQPLMAVFDLPAEPEPVVEGLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASMGALARVQPTPLKNTVDTLAYFRRQGIPVYGAFLDGQSLYEAPLPNFTEPAILVLGSEGRGISPEVAAEITDRLTIPASGLSV----ESLNVAIATAILCSEWRRRS
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
3.1 178-224 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
view details
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
2YY8A 3AI9X 3AIAA 1P9PA 1UAKA 4H3ZA 1O6DA 3N4KA 3GYQA 1K3RA 3L8UA 3NK7A 3DCMX 3NK6A 2QWVA 3IC6A 1V2XA 1X7OA 3KY7A 4FAKA 4IG6A 1UAJA 3AXZA 1V6ZA 1TO0A 1GZ0A 3ONPA 1J85A 3ILKA 2CX8A 1NS5A 2QMMA 3QUVA 3E5YA 4H3YA 1UALA 1VHKA 1VHYA 1X7PA 4CNGB 1MXIA 4CNEB 2I6DA 3IEFA 4E8BA 3N4JA 1NXZA 4CNFB 1VH0A 2HA8A 3KNUA 2O3AA 2Z0YA 1ZJRA 1UAMA 3KTYA
chains in the KnotProt database with same CATH superfamily
2YY8A 3AI9X 3AIAA 1P9PA 1UAKA 4H3ZA 1O6DA 3N4KA 3GYQA 1K3RA 3L8UA 3NK7A 3DCMX 3NK6A 2QWVA 3IC6A 1V2XA 1X7OA 3KY7A 4FAKA 4IG6A 1UAJA 3AXZA 1V6ZA 1TO0A 1GZ0A 3ONPA 1J85A 3ILKA 2CX8A 1NS5A 2QMMA 3QUVA 3E5YA 4H3YA 1UALA 1VHKA 1VHYA 1X7PA 4CNGB 1MXIA 4CNEB 2I6DA 3IEFA 4E8BA 3N4JA 1NXZA 4CNFB 1VH0A 2HA8A 3KNUA 2O3AA 2Z0YA 1ZJRA 1UAMA 3KTYA
chains in the KnotProt database with same CATH topology
2YY8A 3AI9X 3AIAA 1P9PA 1UAKA 4H3ZA 1O6DA 3N4KA 3GYQA 1K3RA 3L8UA 3NK7A 3DCMX 3NK6A 2QWVA 3IC6A 1V2XA 1X7OA 3KY7A 4FAKA 4IG6A 1UAJA 3AXZA 1V6ZA 1TO0A 1GZ0A 3ONPA 1J85A 3ILKA 2CX8A 1NS5A 2QMMA 3QUVA 3E5YA 4H3YA 1UALA 1VHKA 1VHYA 1X7PA 4CNGB 1MXIA 4CNEB 2I6DA 3IEFA 4E8BA 3N4JA 1NXZA 4CNFB 1VH0A 2HA8A 3KNUA 2O3AA 2Z0YA 1ZJRA 1UAMA 3KTYA
chains in the KnotProt database with same CATH homology


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