1VHKA

Crystal structure of an hypothetical protein
Warning
  • Chain breaks within knot 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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Genus: 69
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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+31 171-223 53 1-170, 224-252 170 29 knot
Chain Sequence
QRYFIELTKQQIEEAPTFSITGEEVHHIVNVMRMNEGDQIICCSQDGFEAKCELQSVSKDKVSCLVIEWTNENRELPIKVYIASGLPKGDKLEWIIQKGTELGAHAFIPFQAARSVV---------KRERWTKIAKEAAEQSYRNEVPRVMDVHSFQQLLQRMQDFDKCVVAYESAFSAIVSS--------LPKGSSLLIVFGPEGGLTEAEVERLTEQDGVTCGLGPRILRTETAPLYALSAISYQTELLR
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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3.1 161-207 47 1-160, 208-235 160 28 knot
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3.1 163-209 47 1-160, 232-235 161-162, 210-231 160 4 slipknot
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3.1 164-230 67 1-160, 235-235 161-163, 231-234 160 1 slipknot
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2.1 163-234 72 235-235 1-160 161-162 160 0 slipknot
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3.1 164-211 48 1-162, 231-235 163-163, 212-230 162 5 slipknot
sequence length 252
structure length 235
publication title Structural analysis of a set of proteins resulting from a bacterial genomics project
pubmed doi rcsb
molecule tags Structural genomics, unknown function
molecule keywords Hypothetical protein yqeU
source organism Bacillus subtilis
missing residues 118-126, 175-182
total genus Genus: 69
ec nomenclature ec 2.1.1.193: 16S rRNA (uracil(1498)-N(3))-methyltransferase.
pdb deposition date 2003-12-01
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 1vhkA01
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 1vhkA02
4CNFB 2QMMA 3E5YA 2O3AA 3ILKA 2YY8A 1K3RA 3ONPA 1O6DA 1UAMA 4IG6A 3KY7A 3NK6A 1ZJRA 1X7PA 1NS5A 1VHYA 2HA8A 1VHKA 4H3ZA 1VH0A 3GYQA 3N4KA 3QUVA 3DCMX 3KNUA 3N4JA 3NK7A 1J85A 1NXZA 1MXIA 1X7OA 3IC6A 1TO0A 1V2XA 1P9PA 4FAKA 1UAKA 1V6ZA 3AI9X 1UALA 2I6DA 3KW2A 4CNGB 1GZ0A 3KTYA 2Z0YA 3IEFA 3L8UA 4H3YA 4CNEB 3AXZA 2QWVA 4E8BA 1UAJA 2CX8A 3AIAA
chains in the KnotProt database with same CATH superfamily
4CNFB 2QMMA 3E5YA 2O3AA 3ILKA 2YY8A 1K3RA 3ONPA 1O6DA 1UAMA 4IG6A 3KY7A 3NK6A 1ZJRA 1X7PA 1NS5A 1VHYA 2HA8A 1VHKA 4H3ZA 1VH0A 3GYQA 3N4KA 3QUVA 3DCMX 3KNUA 3N4JA 3NK7A 1J85A 1NXZA 1MXIA 1X7OA 3IC6A 1TO0A 1V2XA 1P9PA 4FAKA 1UAKA 1V6ZA 3AI9X 1UALA 2I6DA 3KW2A 4CNGB 1GZ0A 3KTYA 2Z0YA 3IEFA 3L8UA 4H3YA 4CNEB 3AXZA 2QWVA 4E8BA 1UAJA 2CX8A 3AIAA
chains in the KnotProt database with same CATH topology
4CNFB 2QMMA 3E5YA 2O3AA 3ILKA 2YY8A 1K3RA 3ONPA 1O6DA 1UAMA 4IG6A 3KY7A 3NK6A 1ZJRA 1X7PA 1NS5A 1VHYA 2HA8A 1VHKA 4H3ZA 1VH0A 3GYQA 3N4KA 3QUVA 3DCMX 3KNUA 3N4JA 3NK7A 1J85A 1NXZA 1MXIA 1X7OA 3IC6A 1TO0A 1V2XA 1P9PA 4FAKA 1UAKA 1V6ZA 3AI9X 1UALA 2I6DA 3KW2A 4CNGB 1GZ0A 3KTYA 2Z0YA 3IEFA 3L8UA 4H3YA 4CNEB 3AXZA 2QWVA 4E8BA 1UAJA 2CX8A 3AIAA
chains in the KnotProt database with same CATH homology

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