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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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
3VTKA 4IVPA 1GKUB 4IVRA 1KI8A 1E2IA 1E2JA 1KI7A 4JBYA 3RDPA 1P72A 1F48A 1P75A 1QHIA 1E2NA 1KI2A 2KI5A 1KIMA 1KI6B 1P6XA 1P73A 1P7CA 1VTKA 1E2KA 4IVQA 1E2HA 3F0TA 1KI4A 1E2PA 1KI6A 1OF1A 1II9A 1E2LA 1KI3A 1OSNA 2VTKA 4JBXA 1E2MA
chains in the KnotProt database with same CATH superfamily
3VTKA 4IVPA 3FR8A 1JS1X 1DBIA 1YH1A 2XTJA 3L06A 3M4NA 1GKUB 4IVRA 1KI8A 3KZCA 1QMGA 3M5DA 1E2IA 3L02A 1E2JA 2G7MC 1KI7A 4JBYA 3RDPA 1P72A 1LNSA 3KZNA 3KZMA 3L04A 1F48A 1P75A 1QHIA 1E2NA 1KI2A 2KI5A 3FSGA 1KIMA 1KI6B 1YRLA 1P6XA 1P73A 3KZKA 3L05A 1YVEI 1P7CA 1VTKA 3M4JA 1E2KA 4IVQA 2FG6C 1E2HA 3F0TA 1KI4A 1E2PA 1R4MB 1KI6A 3M5CA 1OF1A 1II9A 3KZOA 1R4NB 1E2LA 1KI3A 1OSNA 2VTKA 3FR7A 4JBXA 1E2MA
chains in the KnotProt database with same CATH topology
3VTKA 4IVPA 1GKUB 4IVRA 1KI8A 1E2IA 1E2JA 1KI7A 4JBYA 3RDPA 1P72A 1F48A 1P75A 1QHIA 1E2NA 1KI2A 2KI5A 1KIMA 1KI6B 1P6XA 1P73A 1P7CA 1VTKA 1E2KA 4IVQA 1E2HA 3F0TA 1KI4A 1E2PA 1KI6A 1OF1A 1II9A 1E2LA 1KI3A 1OSNA 2VTKA 4JBXA 1E2MA
chains in the KnotProt database with same CATH homology


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