1KI3A

Crystal structure of thymidine kinase from herpes simplex virus type i complexed with penciclovir
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Slipknot S +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 5-116 112 1-4 305-329 117-304 4 25 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKTTTTQLLVA-----DIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSAPPPA--LTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSPRPHIGD----------------TLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
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
2.1 8-111 104 1-7 149-306 112-148 7 158 slipknot
view details
2.1 8-150 143 1-7 182-306 151-181 7 125 slipknot
view details
2.1 8-182 175 1-7 281-306 183-280 7 26 slipknot
view details
2.1 6-148 143 1-2, 151-306 3-5, 149-150 2 156 slipknot
view details
2.1 9-195 187 1-7, 277-306 8-8, 196-276 7 30 slipknot
sequence length 329
structure length 306
publication title Exploring the active site of herpes simplex virus type-1 thymidine kinase by X-ray crystallography of complexes with aciclovir and other ligands.
pubmed doi rcsb
molecule tags Phosphotransferase
molecule keywords THYMIDINE KINASE
source organism Herpes simplex virus (type 1 / strain 17)
missing residues 27-31, 105-106, 219-234
total genus Genus: 104
ec nomenclature ec 2.7.1.21: Thymidine kinase.
pdb deposition date 1998-05-15
KnotProt deposition date 2014-07-31

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00693 Herpes_TK Thymidine kinase from herpesvirus
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolases 1ki3A00
1GKUB 4JBXA 1KI8A 4IVRA 1QHIA 4IVQA 1VTKA 1KI6B 4IVPA 1E2LA 1KI6A 1KIMA 1F48A 1KI7A 1P75A 1E2IA 1E2KA 1P7CA 1II9A 1KI2A 1P72A 2KI5A 1OF1A 3VTKA 1E2PA 1OSNA 1P6XA 4JBYA 1KI3A 1P73A 3F0TA 1E2JA 2VTKA 1E2MA 1KI4A 1E2NA 3RDPA 1E2HA
chains in the KnotProt database with same CATH superfamily
1GKUB 4JBXA 1KI8A 2G7MC 3L06A 4IVRA 1QHIA 4IVQA 1VTKA 3FSGA 3M5CA 3FR8A 1KI6B 2XTJA 4IVPA 1E2LA 3KZMA 1YRLA 3KZCA 1KI6A 1KIMA 1F48A 1KI7A 1P75A 1E2IA 1E2KA 1P7CA 1II9A 1YH1A 1KI2A 1P72A 2KI5A 3M4JA 1OF1A 3VTKA 1E2PA 1OSNA 1P6XA 2FG6C 1KI3A 1P73A 4JBYA 3M5DA 1YVEI 3L02A 3L05A 3F0TA 1R4NB 3M4NA 1E2JA 2VTKA 1R4MB 3KZKA 3FR7A 1E2MA 1KI4A 1E2NA 1JS1X 1DBIA 1QMGA 3KZOA 3KZNA 3RDPA 1E2HA 1LNSA 3L04A
chains in the KnotProt database with same CATH topology
1GKUB 4JBXA 1KI8A 4IVRA 1QHIA 4IVQA 1VTKA 1KI6B 4IVPA 1E2LA 1KI6A 1KIMA 1F48A 1KI7A 1P75A 1E2IA 1E2KA 1P7CA 1II9A 1KI2A 1P72A 2KI5A 1OF1A 3VTKA 1E2PA 1OSNA 1P6XA 4JBYA 1KI3A 1P73A 3F0TA 1E2JA 2VTKA 1E2MA 1KI4A 1E2NA 3RDPA 1E2HA
chains in the KnotProt database with same CATH homology


 
#chains in the KnotProt database with same CATH superfamily
 1GKU B;  4JBX A;  1KI8 A;  4IVR A;  1QHI A;  4IVQ A;  1VTK A;  1KI6 B;  4IVP A;  1E2L A;  1KI6 A;  1KIM A;  1F48 A;  1KI7 A;  1P75 A;  1E2I A;  1E2K A;  1P7C A;  1II9 A;  1KI2 A;  1P72 A;  2KI5 A;  1OF1 A;  3VTK A;  1E2P A;  1OSN A;  1P6X A;  4JBY A;  1KI3 A;  1P73 A;  3F0T A;  1E2J A;  2VTK A;  1E2M A;  1KI4 A;  1E2N A;  3RDP A;  1E2H A; 
#chains in the KnotProt database with same CATH topology
 1GKU B;  4JBX A;  1KI8 A;  2G7M C;  3L06 A;  4IVR A;  1QHI A;  4IVQ A;  1VTK A;  3FSG A;  3M5C A;  3FR8 A;  1KI6 B;  2XTJ A;  4IVP A;  1E2L A;  3KZM A;  1YRL A;  3KZC A;  1KI6 A;  1KIM A;  1F48 A;  1KI7 A;  1P75 A;  1E2I A;  1E2K A;  1P7C A;  1II9 A;  1YH1 A;  1KI2 A;  1P72 A;  2KI5 A;  3M4J A;  1OF1 A;  3VTK A;  1E2P A;  1OSN A;  1P6X A;  2FG6 C;  1KI3 A;  1P73 A;  4JBY A;  3M5D A;  1YVE I;  3L02 A;  3L05 A;  3F0T A;  1R4N B;  3M4N A;  1E2J A;  2VTK A;  1R4M B;  3KZK A;  3FR7 A;  1E2M A;  1KI4 A;  1E2N A;  1JS1 X;  1DBI A;  1QMG A;  3KZO A;  3KZN A;  3RDP A;  1E2H A;  1LNS A;  3L04 A; 
#chains in the KnotProt database with same CATH homology
 1GKU B;  4JBX A;  1KI8 A;  4IVR A;  1QHI A;  4IVQ A;  1VTK A;  1KI6 B;  4IVP A;  1E2L A;  1KI6 A;  1KIM A;  1F48 A;  1KI7 A;  1P75 A;  1E2I A;  1E2K A;  1P7C A;  1II9 A;  1KI2 A;  1P72 A;  2KI5 A;  1OF1 A;  3VTK A;  1E2P A;  1OSN A;  1P6X A;  4JBY A;  1KI3 A;  1P73 A;  3F0T A;  1E2J A;  2VTK A;  1E2M A;  1KI4 A;  1E2N A;  3RDP A;  1E2H 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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