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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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

  Help Knotting data interpretation Full screen
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

  Help Knotoid data interpretation Full screen
Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1


  Help Knotoid subchains data interpretation Full screen
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
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
4H3ZA 1VHYA 1GZ0A 1J85A 2Z0YA 2I6DA 2O3AA 3AIAA 4CNGB 1MXIA 2QMMA 1TO0A 3N4JA 1UAKA 4FAKA 4IG6A 2HA8A 1UAMA 3KTYA 1K3RA 3QUVA 1P9PA 1V2XA 3ILKA 3KY7A 3IEFA 3GYQA 3L8UA 1VHKA 3KW2A 4CNEB 3NK6A 3IC6A 1VH0A 3N4KA 2YY8A 1V6ZA 4CNFB 1UAJA 4H3YA 2CX8A 1ZJRA 1X7OA 1X7PA 1UALA 3E5YA 1NXZA 3KNUA 3AI9X 3NK7A 3AXZA 3DCMX 1O6DA 2QWVA 1NS5A 3ONPA 4E8BA
chains in the KnotProt database with same CATH superfamily
4H3ZA 1VHYA 1GZ0A 1J85A 2Z0YA 2I6DA 2O3AA 3AIAA 4CNGB 1MXIA 2QMMA 1TO0A 3N4JA 1UAKA 4FAKA 4IG6A 2HA8A 1UAMA 3KTYA 1K3RA 3QUVA 1P9PA 1V2XA 3ILKA 3KY7A 3IEFA 3GYQA 3L8UA 1VHKA 3KW2A 4CNEB 3NK6A 3IC6A 1VH0A 3N4KA 2YY8A 1V6ZA 4CNFB 1UAJA 4H3YA 2CX8A 1ZJRA 1X7OA 1X7PA 1UALA 3E5YA 1NXZA 3KNUA 3AI9X 3NK7A 3AXZA 3DCMX 1O6DA 2QWVA 1NS5A 3ONPA 4E8BA
chains in the KnotProt database with same CATH topology
4H3ZA 1VHYA 1GZ0A 1J85A 2Z0YA 2I6DA 2O3AA 3AIAA 4CNGB 1MXIA 2QMMA 1TO0A 3N4JA 1UAKA 4FAKA 4IG6A 2HA8A 1UAMA 3KTYA 1K3RA 3QUVA 1P9PA 1V2XA 3ILKA 3KY7A 3IEFA 3GYQA 3L8UA 1VHKA 3KW2A 4CNEB 3NK6A 3IC6A 1VH0A 3N4KA 2YY8A 1V6ZA 4CNFB 1UAJA 4H3YA 2CX8A 1ZJRA 1X7OA 1X7PA 1UALA 3E5YA 1NXZA 3KNUA 3AI9X 3NK7A 3AXZA 3DCMX 1O6DA 2QWVA 1NS5A 3ONPA 4E8BA
chains in the KnotProt database with same CATH homology

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

  
#similar chains in the KnotProt database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...
How to cite
KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling