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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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


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