1X7PA

Crystal structure of the spou methyltransferase avirb from streptomyces viridochromogenes in complex with the cofactor adomet
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
+31 192-232 41 1-191, 233-265 191 33 knot
Chain Sequence
RNARFQQWQALLGNRNKRTRAGEFLVMGVRPISLAVEHGWPVRTLLYDGQRELSKWARELLRTVRTEQIAMAPDLLMELGEKNEAPPEVVAVVEMPADDLDRIPVREDFLGVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAADVYDPKSVRSSTGSLFSLPAVRVPSPGEVMDWVEARRAAGTPIVLVGTDEHGDCDVFDFDFTQPTLLLIGNETAGLSNAWRTLCDYTVSIPMAGSASSLNAANAATAILYEAVRQRISGR
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
3.1 191-233 43 1-190, 234-265 190 32 knot
view details
2.1 190-230 41 1-189 236-265 231-235 189 30 slipknot
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3.1 192-234 43 235-265 1-190 191-191 190 30 slipknot
view details
3.1 193-242 50 1-191, 252-265 192-192, 243-251 191 14 slipknot
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3.1 193-236 44 1-191, 242-265 192-192, 237-241 191 24 slipknot
view details
3.1 193-252 60 253-265 1-191 192-192 191 12 slipknot
view details
2.1 194-253 60 1-192, 263-265 193-193, 254-262 192 3 slipknot
sequence length 265
structure length 265
publication title Structure and function of the antibiotic resistance-mediating methyltransferase AviRb from Streptomyces viridochromogenes
pubmed doi rcsb
molecule tags Transferase
molecule keywords rRNA methyltransferase
source organism Streptomyces viridochromogenes
total genus Genus: 86
ec nomenclature ec 2.1.1.208: 23S rRNA (uridine(2479)-2'-O)-methyltransferase.
pdb deposition date 2004-08-16
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; 1x7pA01
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 1x7pA02
3NK7A 1J85A 4FAKA 3KNUA 4CNFB 1TO0A 2HA8A 1K3RA 2QWVA 1VH0A 2CX8A 3L8UA 4CNEB 1UAKA 1UAMA 2O3AA 2I6DA 3E5YA 1V2XA 2YY8A 3N4KA 1X7PA 3AXZA 3NK6A 4IG6A 4H3YA 4H3ZA 1V6ZA 1UALA 1X7OA 3IC6A 3ONPA 2QMMA 3QUVA 3GYQA 1NS5A 3KY7A 1O6DA 4E8BA 1GZ0A 3IEFA 1ZJRA 1P9PA 1UAJA 3DCMX 2Z0YA 3KTYA 1VHYA 3N4JA 3AI9X 3ILKA 4CNGB 1VHKA 1MXIA 1NXZA 3AIAA
chains in the KnotProt database with same CATH superfamily
3NK7A 1J85A 4FAKA 3KNUA 4CNFB 1TO0A 2HA8A 1K3RA 2QWVA 1VH0A 2CX8A 3L8UA 4CNEB 1UAKA 1UAMA 2O3AA 2I6DA 3E5YA 1V2XA 2YY8A 3N4KA 1X7PA 3AXZA 3NK6A 4IG6A 4H3YA 4H3ZA 1V6ZA 1UALA 1X7OA 3IC6A 3ONPA 2QMMA 3QUVA 3GYQA 1NS5A 3KY7A 1O6DA 4E8BA 1GZ0A 3IEFA 1ZJRA 1P9PA 1UAJA 3DCMX 2Z0YA 3KTYA 1VHYA 3N4JA 3AI9X 3ILKA 4CNGB 1VHKA 1MXIA 1NXZA 3AIAA
chains in the KnotProt database with same CATH topology
3NK7A 1J85A 4FAKA 3KNUA 4CNFB 1TO0A 2HA8A 1K3RA 2QWVA 1VH0A 2CX8A 3L8UA 4CNEB 1UAKA 1UAMA 2O3AA 2I6DA 3E5YA 1V2XA 2YY8A 3N4KA 1X7PA 3AXZA 3NK6A 4IG6A 4H3YA 4H3ZA 1V6ZA 1UALA 1X7OA 3IC6A 3ONPA 2QMMA 3QUVA 3GYQA 1NS5A 3KY7A 1O6DA 4E8BA 1GZ0A 3IEFA 1ZJRA 1P9PA 1UAJA 3DCMX 2Z0YA 3KTYA 1VHYA 3N4JA 3AI9X 3ILKA 4CNGB 1VHKA 1MXIA 1NXZA 3AIAA
chains in the KnotProt database with same CATH homology


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