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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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
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
3GYQA 3AXZA 4H3ZA 1UALA 4FAKA 1VHYA 3KTYA 1ZJRA 3IC6A 3N4JA 1O6DA 2QMMA 3KW2A 3ILKA 3N4KA 4E8BA 1X7PA 3KNUA 1MXIA 3L8UA 3ONPA 3AI9X 1K3RA 3E5YA 1GZ0A 3NK7A 4IG6A 1TO0A 1NS5A 1V6ZA 3KY7A 3NK6A 4CNFB 4CNEB 2Z0YA 2YY8A 1IPAA 3QUVA 3IEFA 1UAKA 1NXZA 2HA8A 2I6DA 1V2XA 2QWVA 4H3YA 3AIAA 1VHKA 1J85A 1UAMA 2CX8A 1VH0A 1UAJA 1X7OA 1P9PA 3DCMX 4CNGB 2O3AA
chains in the KnotProt database with same CATH superfamily
3GYQA 3AXZA 4H3ZA 1UALA 4FAKA 1VHYA 3KTYA 1ZJRA 3IC6A 3N4JA 1O6DA 2QMMA 3KW2A 3ILKA 3N4KA 4E8BA 1X7PA 3KNUA 1MXIA 3L8UA 3ONPA 3AI9X 1K3RA 3E5YA 1GZ0A 3NK7A 4IG6A 1TO0A 1NS5A 1V6ZA 3KY7A 3NK6A 4CNFB 4CNEB 2Z0YA 2YY8A 1IPAA 3QUVA 3IEFA 1UAKA 1NXZA 2HA8A 2I6DA 1V2XA 2QWVA 4H3YA 3AIAA 1VHKA 1J85A 1UAMA 2CX8A 1VH0A 1UAJA 1X7OA 1P9PA 3DCMX 4CNGB 2O3AA
chains in the KnotProt database with same CATH topology
3GYQA 3AXZA 4H3ZA 1UALA 4FAKA 1VHYA 3KTYA 1ZJRA 3IC6A 3N4JA 1O6DA 2QMMA 3KW2A 3ILKA 3N4KA 4E8BA 1X7PA 3KNUA 1MXIA 3L8UA 3ONPA 3AI9X 1K3RA 3E5YA 1GZ0A 3NK7A 4IG6A 1TO0A 1NS5A 1V6ZA 3KY7A 3NK6A 4CNFB 4CNEB 2Z0YA 2YY8A 1IPAA 3QUVA 3IEFA 1UAKA 1NXZA 2HA8A 2I6DA 1V2XA 2QWVA 4H3YA 3AIAA 1VHKA 1J85A 1UAMA 2CX8A 1VH0A 1UAJA 1X7OA 1P9PA 3DCMX 4CNGB 2O3AA
chains in the KnotProt database with same CATH homology


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