3F0TA

Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with n-methyl-dhbt
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 6-118 113 1-5 307-329 119-306 5 23 slipknot
Chain Sequence
KMPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEA-----PPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGPRPHI---------------GDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMG
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 8-113 106 1-7 152-309 114-151 7 158 slipknot
view details
3.1 8-152 145 1-7 249-309 153-248 7 61 slipknot
view details
3.1 8-248 241 1-7 257-309 249-256 7 53 slipknot
view details
2.1 9-161 153 1-7, 244-309 8-8, 162-243 7 66 slipknot
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2.1 9-252 244 1-7, 257-309 8-8, 253-256 7 53 slipknot
view details
2.1 9-256 248 1-2, 285-309 3-8, 257-284 2 25 slipknot
sequence length 329
structure length 309
publication title Synthesis, crystal structure, and in vitro biological evaluation of C-6 pyrimidine derivatives: new lead structures for monitoring gene expression in vivo.
pubmed doi rcsb
molecule tags Transferase
molecule keywords Thymidine kinase
source organism Herpes simplex virus (type 1 / strain 17)
missing residues 104-108, 221-235
total genus Genus: 109
ec nomenclature ec 2.7.1.21: Thymidine kinase.
pdb deposition date 2008-10-26
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 3f0tA00
1E2HA 1E2LA 3VTKA 4IVQA 1P73A 1KIMA 1KI3A 4IVRA 3RDPA 1E2KA 1E2PA 1KI2A 1KI6A 1OSNA 1QHIA 2KI5A 1KI6B 1II9A 1E2IA 4JBYA 1P75A 4IVPA 2VTKA 1OF1A 1P72A 1KI4A 1KI8A 1KI7A 1E2MA 1P6XA 1E2NA 4JBXA 1F48A 1E2JA 3F0TA 1VTKA 1P7CA 1GKUB
chains in the KnotProt database with same CATH superfamily
1E2HA 1E2LA 1R4NB 3VTKA 4IVQA 3L04A 3M5DA 1P73A 3M4NA 1KIMA 1KI3A 4IVRA 3KZKA 3RDPA 3L02A 1YH1A 2FG7X 1E2KA 1E2PA 1DBIA 2G7MC 1KI2A 1KI6A 1OSNA 3FR8A 1QHIA 2KI5A 3KZMA 2FG7C 1KI6B 1II9A 3FR7A 2XTJA 1QMGA 1E2IA 3KZOA 1JS1X 3M4JA 2FG6C 1P75A 4JBYA 3KZNA 1R4MB 1LNSA 4IVPA 1YRLA 2VTKA 1OF1A 1P72A 1KI4A 1KI8A 1KI7A 1E2MA 3KZCA 3M5CA 1P6XA 1E2NA 4JBXA 1F48A 3L05A 1YVEI 1E2JA 3F0TA 3FSGA 1VTKA 1P7CA 3L06A 1GKUB
chains in the KnotProt database with same CATH topology
1E2HA 1E2LA 3VTKA 4IVQA 1P73A 1KIMA 1KI3A 4IVRA 3RDPA 1E2KA 1E2PA 1KI2A 1KI6A 1OSNA 1QHIA 2KI5A 1KI6B 1II9A 1E2IA 4JBYA 1P75A 4IVPA 2VTKA 1OF1A 1P72A 1KI4A 1KI8A 1KI7A 1E2MA 1P6XA 1E2NA 4JBXA 1F48A 1E2JA 3F0TA 1VTKA 1P7CA 1GKUB
chains in the KnotProt database with same CATH homology


 
#chains in the KnotProt database with same CATH superfamily
 1E2H A;  1E2L A;  3VTK A;  4IVQ A;  1P73 A;  1KIM A;  1KI3 A;  4IVR A;  3RDP A;  1E2K A;  1E2P A;  1KI2 A;  1KI6 A;  1OSN A;  1QHI A;  2KI5 A;  1KI6 B;  1II9 A;  1E2I A;  4JBY A;  1P75 A;  4IVP A;  2VTK A;  1OF1 A;  1P72 A;  1KI4 A;  1KI8 A;  1KI7 A;  1E2M A;  1P6X A;  1E2N A;  4JBX A;  1F48 A;  1E2J A;  3F0T A;  1VTK A;  1P7C A;  1GKU B; 
#chains in the KnotProt database with same CATH topology
 1E2H A;  1E2L A;  1R4N B;  3VTK A;  4IVQ A;  3L04 A;  3M5D A;  1P73 A;  3M4N A;  1KIM A;  1KI3 A;  4IVR A;  3KZK A;  3RDP A;  3L02 A;  1YH1 A;  2FG7 X;  1E2K A;  1E2P A;  1DBI A;  2G7M C;  1KI2 A;  1KI6 A;  1OSN A;  3FR8 A;  1QHI A;  2KI5 A;  3KZM A;  2FG7 C;  1KI6 B;  1II9 A;  3FR7 A;  2XTJ A;  1QMG A;  1E2I A;  3KZO A;  1JS1 X;  3M4J A;  2FG6 C;  1P75 A;  4JBY A;  3KZN A;  1R4M B;  1LNS A;  4IVP A;  1YRL A;  2VTK A;  1OF1 A;  1P72 A;  1KI4 A;  1KI8 A;  1KI7 A;  1E2M A;  3KZC A;  3M5C A;  1P6X A;  1E2N A;  4JBX A;  1F48 A;  3L05 A;  1YVE I;  1E2J A;  3F0T A;  3FSG A;  1VTK A;  1P7C A;  3L06 A;  1GKU B; 
#chains in the KnotProt database with same CATH homology
 1E2H A;  1E2L A;  3VTK A;  4IVQ A;  1P73 A;  1KIM A;  1KI3 A;  4IVR A;  3RDP A;  1E2K A;  1E2P A;  1KI2 A;  1KI6 A;  1OSN A;  1QHI A;  2KI5 A;  1KI6 B;  1II9 A;  1E2I A;  4JBY A;  1P75 A;  4IVP A;  2VTK A;  1OF1 A;  1P72 A;  1KI4 A;  1KI8 A;  1KI7 A;  1E2M A;  1P6X A;  1E2N A;  4JBX A;  1F48 A;  1E2J A;  3F0T A;  1VTK A;  1P7C A;  1GKU B; 
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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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