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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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


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