1NXZA

X-ray crystal structure of protein yggj_haein of haemophilus influenzae. northeast structural genomics consortium target ir73.
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
+31 169-214 46 1-168, 215-246 168 32 knot
Chain Sequence
RIPRIYHPISLENQTQCYLSEDAANHVARVLRMTEGEQLELFDGSNHIYPAKIIESNKKSVKVEILGRELADKESHLKIHLGQVISRGERMEFTIQKSVELGVNVITPLWSERCGVKLDAERMDKKIQQWQKIAIAACEQCGRNIVPEIRPLMKLQDWCAENDGALKLNLHPRAHYSIKTLPTIPAGGVRLLIGSEGGLSAQEIAQTEQQGFTEILLGKRVLRTETASLAAISALQICFGDLGEAA
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
3.1 167-215 49 1-166, 216-246 166 31 knot
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2.1 159-211 53 1-158 218-246 212-217 158 29 slipknot
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3.1 168-215 48 1-166, 231-246 167-167, 216-230 166 16 slipknot
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3.1 170-217 48 1-166, 236-246 167-169, 218-235 166 11 slipknot
view details
2.1 170-241 72 242-246 1-166 167-169 166 4 slipknot
sequence length 246
structure length 246
publication title Functional assignment based on structural analysis: crystal structure of the yggJ protein (HI0303) of Haemophilus influenzae reveals an RNA methyltransferase with a deep trefoil knot.
pubmed doi rcsb
molecule tags Structural genomics, unknown function
molecule keywords Hypothetical protein HI0303
source organism Haemophilus influenzae
total genus Genus: 67
ec nomenclature ec 2.1.1.193: 16S rRNA (uracil(1498)-N(3))-methyltransferase.
pdb deposition date 2003-02-11
KnotProt deposition date 2014-07-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF04452 Methyltrans_RNA RNA methyltransferase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.40.240.20 Mainly Beta Beta Barrel Ribosomal Protein L25; Chain P Hypothetical PUA domain-like; domain 1 1nxzA01
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 1nxzA02
1O6DA 1VHKA 2YY8A 3AXZA 1VH0A 4E8BA 2QWVA 1V2XA 1GZ0A 2HA8A 2CX8A 1VHYA 1X7OA 1UAKA 3KW2A 1NS5A 1UALA 3QUVA 4CNFB 1V6ZA 1X7PA 3GYQA 1K3RA 1UAMA 3ILKA 3KY7A 4H3ZA 3AI9X 1P9PA 3DCMX 3N4JA 2QMMA 3NK6A 1UAJA 1NXZA 1TO0A 3NK7A 3ONPA 3N4KA 2O3AA 4FAKA 4H3YA 2Z0YA 1ZJRA 1MXIA 3IEFA 1J85A 4CNGB 3E5YA 3KNUA 4CNEB 3KTYA 2I6DA 3AIAA 3L8UA 4IG6A 3IC6A
chains in the KnotProt database with same CATH superfamily
1O6DA 1VHKA 2YY8A 3AXZA 1VH0A 4E8BA 2QWVA 1V2XA 1GZ0A 2HA8A 2CX8A 1VHYA 1X7OA 1UAKA 3KW2A 1NS5A 1UALA 3QUVA 4CNFB 1V6ZA 1X7PA 3GYQA 1K3RA 1UAMA 3ILKA 3KY7A 4H3ZA 3AI9X 1P9PA 3DCMX 3N4JA 2QMMA 3NK6A 1UAJA 1NXZA 1TO0A 3NK7A 3ONPA 3N4KA 2O3AA 4FAKA 4H3YA 2Z0YA 1ZJRA 1MXIA 3IEFA 1J85A 4CNGB 3E5YA 3KNUA 4CNEB 3KTYA 2I6DA 3AIAA 3L8UA 4IG6A 3IC6A
chains in the KnotProt database with same CATH topology
1O6DA 1VHKA 2YY8A 3AXZA 1VH0A 4E8BA 2QWVA 1V2XA 1GZ0A 2HA8A 2CX8A 1VHYA 1X7OA 1UAKA 3KW2A 1NS5A 1UALA 3QUVA 4CNFB 1V6ZA 1X7PA 3GYQA 1K3RA 1UAMA 3ILKA 3KY7A 4H3ZA 3AI9X 1P9PA 3DCMX 3N4JA 2QMMA 3NK6A 1UAJA 1NXZA 1TO0A 3NK7A 3ONPA 3N4KA 2O3AA 4FAKA 4H3YA 2Z0YA 1ZJRA 1MXIA 3IEFA 1J85A 4CNGB 3E5YA 3KNUA 4CNEB 3KTYA 2I6DA 3AIAA 3L8UA 4IG6A 3IC6A
chains in the KnotProt database with same CATH homology


 
#chains in the KnotProt database with same CATH superfamily
 1O6D A;  1VHK A;  2YY8 A;  3AXZ A;  1VH0 A;  4E8B A;  2QWV A;  1V2X A;  1GZ0 A;  2HA8 A;  2CX8 A;  1VHY A;  1X7O A;  1UAK A;  3KW2 A;  1NS5 A;  1UAL A;  3QUV A;  4CNF B;  1V6Z A;  1X7P A;  3GYQ A;  1K3R A;  1UAM A;  3ILK A;  3KY7 A;  4H3Z A;  3AI9 X;  1P9P A;  3DCM X;  3N4J A;  2QMM A;  3NK6 A;  1UAJ A;  1NXZ A;  1TO0 A;  3NK7 A;  3ONP A;  3N4K A;  2O3A A;  4FAK A;  4H3Y A;  2Z0Y A;  1ZJR A;  1MXI A;  3IEF A;  1J85 A;  4CNG B;  3E5Y A;  3KNU A;  4CNE B;  3KTY A;  2I6D A;  3AIA A;  3L8U A;  4IG6 A;  3IC6 A; 
#chains in the KnotProt database with same CATH topology
 1O6D A;  1VHK A;  2YY8 A;  3AXZ A;  1VH0 A;  4E8B A;  2QWV A;  1V2X A;  1GZ0 A;  2HA8 A;  2CX8 A;  1VHY A;  1X7O A;  1UAK A;  3KW2 A;  1NS5 A;  1UAL A;  3QUV A;  4CNF B;  1V6Z A;  1X7P A;  3GYQ A;  1K3R A;  1UAM A;  3ILK A;  3KY7 A;  4H3Z A;  3AI9 X;  1P9P A;  3DCM X;  3N4J A;  2QMM A;  3NK6 A;  1UAJ A;  1NXZ A;  1TO0 A;  3NK7 A;  3ONP A;  3N4K A;  2O3A A;  4FAK A;  4H3Y A;  2Z0Y A;  1ZJR A;  1MXI A;  3IEF A;  1J85 A;  4CNG B;  3E5Y A;  3KNU A;  4CNE B;  3KTY A;  2I6D A;  3AIA A;  3L8U A;  4IG6 A;  3IC6 A; 
#chains in the KnotProt database with same CATH homology
 1O6D A;  1VHK A;  2YY8 A;  3AXZ A;  1VH0 A;  4E8B A;  2QWV A;  1V2X A;  1GZ0 A;  2HA8 A;  2CX8 A;  1VHY A;  1X7O A;  1UAK A;  3KW2 A;  1NS5 A;  1UAL A;  3QUV A;  4CNF B;  1V6Z A;  1X7P A;  3GYQ A;  1K3R A;  1UAM A;  3ILK A;  3KY7 A;  4H3Z A;  3AI9 X;  1P9P A;  3DCM X;  3N4J A;  2QMM A;  3NK6 A;  1UAJ A;  1NXZ A;  1TO0 A;  3NK7 A;  3ONP A;  3N4K A;  2O3A A;  4FAK A;  4H3Y A;  2Z0Y A;  1ZJR A;  1MXI A;  3IEF A;  1J85 A;  4CNG B;  3E5Y A;  3KNU A;  4CNE B;  3KTY A;  2I6D A;  3AIA A;  3L8U A;  4IG6 A;  3IC6 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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