1X7PA

Crystal structure of the spou methyltransferase avirb from streptomyces viridochromogenes in complex with the cofactor adomet
Genus: 86
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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+31 192-232 41 1-191, 233-265 191 33 knot
Chain Sequence
RNARFQQWQALLGNRNKRTRAGEFLVMGVRPISLAVEHGWPVRTLLYDGQRELSKWARELLRTVRTEQIAMAPDLLMELGEKNEAPPEVVAVVEMPADDLDRIPVREDFLGVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAADVYDPKSVRSSTGSLFSLPAVRVPSPGEVMDWVEARRAAGTPIVLVGTDEHGDCDVFDFDFTQPTLLLIGNETAGLSNAWRTLCDYTVSIPMAGSASSLNAANAATAILYEAVRQRISGR
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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3.1 191-233 43 1-190, 234-265 190 32 knot
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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
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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
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3.1 193-252 60 253-265 1-191 192-192 191 12 slipknot
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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
2QWVA 2QMMA 3DCMX 1VH0A 3KNUA 3KTYA 1UAJA 2I6DA 2Z0YA 4FAKA 3AI9X 3QUVA 3KY7A 2HA8A 4CNFB 1V6ZA 1VHYA 2YY8A 1K3RA 1X7OA 2CX8A 1J85A 3ILKA 3L8UA 3E5YA 4IG6A 4CNGB 1VHKA 4H3YA 2O3AA 3AXZA 1O6DA 1V2XA 3N4KA 4H3ZA 3NK6A 1UAKA 1UAMA 1UALA 3N4JA 1X7PA 3GYQA 3NK7A 1NXZA 3IC6A 3ONPA 4CNEB 3AIAA 1ZJRA 3IEFA 4E8BA 1MXIA 1P9PA 1NS5A 1TO0A 1GZ0A
chains in the KnotProt database with same CATH superfamily
2QWVA 2QMMA 3DCMX 1VH0A 3KNUA 3KTYA 1UAJA 2I6DA 2Z0YA 4FAKA 3AI9X 3QUVA 3KY7A 2HA8A 4CNFB 1V6ZA 1VHYA 2YY8A 1K3RA 1X7OA 2CX8A 1J85A 3ILKA 3L8UA 3E5YA 4IG6A 4CNGB 1VHKA 4H3YA 2O3AA 3AXZA 1O6DA 1V2XA 3N4KA 4H3ZA 3NK6A 1UAKA 1UAMA 1UALA 3N4JA 1X7PA 3GYQA 3NK7A 1NXZA 3IC6A 3ONPA 4CNEB 3AIAA 1ZJRA 3IEFA 4E8BA 1MXIA 1P9PA 1NS5A 1TO0A 1GZ0A
chains in the KnotProt database with same CATH topology
2QWVA 2QMMA 3DCMX 1VH0A 3KNUA 3KTYA 1UAJA 2I6DA 2Z0YA 4FAKA 3AI9X 3QUVA 3KY7A 2HA8A 4CNFB 1V6ZA 1VHYA 2YY8A 1K3RA 1X7OA 2CX8A 1J85A 3ILKA 3L8UA 3E5YA 4IG6A 4CNGB 1VHKA 4H3YA 2O3AA 3AXZA 1O6DA 1V2XA 3N4KA 4H3ZA 3NK6A 1UAKA 1UAMA 1UALA 3N4JA 1X7PA 3GYQA 3NK7A 1NXZA 3IC6A 3ONPA 4CNEB 3AIAA 1ZJRA 3IEFA 4E8BA 1MXIA 1P9PA 1NS5A 1TO0A 1GZ0A
chains in the KnotProt database with same CATH homology

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