1NXZA

X-ray crystal structure of protein yggj_haein of haemophilus influenzae. northeast structural genomics consortium target ir73.
Warning
  • Chain breaks within knotoid 31 (displayed as a gray area on the plot and as '-' on the sequence). The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
  • Chain breaks within knotoid 41 (displayed as a gray area on the plot and as '-' on the sequence). The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Genus: 67
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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+31 169-214 46 1-168, 215-246 168 32 knot
Chain Sequence
RIPRIYHPISLENQTQCYLSEDAANHVARVLRMTEGEQLELFDGSNHIYPAKIIESNKKSVKVEILGRELADKESHLKIHLGQVISRGERMEFTIQKSVELGVNVITPLWSERCGVKLDAERMDKKIQQWQKIAIAACEQCGRNIVPEIRPLMKLQDWCAENDGALKLNLHPRAHYSIKTLPTIPAGGVRLLIGSEGGLSAQEIAQTEQQGFTEILLGKRVLRTETASLAAISALQICFGDLGEAA
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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3.1 167-215 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
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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
2QWVA 1P9PA 3KTYA 4CNFB 1TO0A 2YY8A 3NK7A 1J85A 1UAKA 2HA8A 1X7OA 1UALA 3AXZA 4IG6A 1V6ZA 3KY7A 4H3ZA 3AIAA 3L8UA 1VHYA 3AI9X 1VH0A 3KW2A 1GZ0A 2QMMA 4CNEB 1NXZA 2CX8A 1VHKA 1K3RA 3KNUA 2I6DA 3NK6A 3N4JA 3DCMX 2O3AA 3N4KA 1V2XA 3IC6A 3ONPA 1MXIA 1UAMA 1O6DA 3QUVA 4FAKA 3IEFA 4H3YA 3GYQA 3ILKA 2Z0YA 1ZJRA 1NS5A 3E5YA 4E8BA 1X7PA 4CNGB 1UAJA
chains in the KnotProt database with same CATH superfamily
2QWVA 1P9PA 3KTYA 4CNFB 1TO0A 2YY8A 3NK7A 1J85A 1UAKA 2HA8A 1X7OA 1UALA 3AXZA 4IG6A 1V6ZA 3KY7A 4H3ZA 3AIAA 3L8UA 1VHYA 3AI9X 1VH0A 3KW2A 1GZ0A 2QMMA 4CNEB 1NXZA 2CX8A 1VHKA 1K3RA 3KNUA 2I6DA 3NK6A 3N4JA 3DCMX 2O3AA 3N4KA 1V2XA 3IC6A 3ONPA 1MXIA 1UAMA 1O6DA 3QUVA 4FAKA 3IEFA 4H3YA 3GYQA 3ILKA 2Z0YA 1ZJRA 1NS5A 3E5YA 4E8BA 1X7PA 4CNGB 1UAJA
chains in the KnotProt database with same CATH topology
2QWVA 1P9PA 3KTYA 4CNFB 1TO0A 2YY8A 3NK7A 1J85A 1UAKA 2HA8A 1X7OA 1UALA 3AXZA 4IG6A 1V6ZA 3KY7A 4H3ZA 3AIAA 3L8UA 1VHYA 3AI9X 1VH0A 3KW2A 1GZ0A 2QMMA 4CNEB 1NXZA 2CX8A 1VHKA 1K3RA 3KNUA 2I6DA 3NK6A 3N4JA 3DCMX 2O3AA 3N4KA 1V2XA 3IC6A 3ONPA 1MXIA 1UAMA 1O6DA 3QUVA 4FAKA 3IEFA 4H3YA 3GYQA 3ILKA 2Z0YA 1ZJRA 1NS5A 3E5YA 4E8BA 1X7PA 4CNGB 1UAJA
chains in the KnotProt database with same CATH homology

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