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

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