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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Genus: 109
Slipknot S +31

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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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+31 6-118 113 1-5 307-329 119-306 5 23 slipknot
Chain Sequence
KMPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEA-----PPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGPRPHI---------------GDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMG
Whole chain analysis

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Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1


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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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2.1 8-113 106 1-7 152-309 114-151 7 158 slipknot
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3.1 8-152 145 1-7 249-309 153-248 7 61 slipknot
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3.1 8-248 241 1-7 257-309 249-256 7 53 slipknot
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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
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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
1GKUB 1II9A 1KI2A 1KIMA 1KI7A 1QHIA 1E2NA 1KI3A 1VTKA 1KI6A 1KI6B 1KI4A 2KI5A 1F48A 4JBYA 1P7CA 1P72A 1E2LA 1E2IA 4IVQA 1KI8A 1P73A 2VTKA 1OSNA 1E2HA 1E2PA 1P75A 4JBXA 1E2KA 4IVRA 3RDPA 3F0TA 4IVPA 1P6XA 1E2MA 1OF1A 1E2JA 3VTKA
chains in the KnotProt database with same CATH superfamily
3L05A 1GKUB 1II9A 1KI2A 1KIMA 1KI7A 1QHIA 1E2NA 1KI3A 1VTKA 3M4NA 1YVEI 3KZNA 1KI6A 2G7MC 1KI6B 1KI4A 2KI5A 2XTJA 1F48A 4JBYA 1P7CA 1P72A 1LNSA 3L04A 1E2LA 1E2IA 1YH1A 4IVQA 3FR8A 1JS1X 3KZKA 1KI8A 1P73A 3FR7A 2VTKA 1OSNA 3L02A 3M4JA 1E2HA 1E2PA 1P75A 3L06A 3M5CA 3KZOA 4JBXA 1E2KA 2FG6C 1R4MB 4IVRA 3RDPA 3KZCA 3F0TA 3M5DA 4IVPA 1P6XA 1E2MA 1OF1A 3KZMA 1R4NB 1E2JA 3VTKA 1DBIA 1QMGA 3FSGA 1YRLA
chains in the KnotProt database with same CATH topology
1GKUB 1II9A 1KI2A 1KIMA 1KI7A 1QHIA 1E2NA 1KI3A 1VTKA 1KI6A 1KI6B 1KI4A 2KI5A 1F48A 4JBYA 1P7CA 1P72A 1E2LA 1E2IA 4IVQA 1KI8A 1P73A 2VTKA 1OSNA 1E2HA 1E2PA 1P75A 4JBXA 1E2KA 4IVRA 3RDPA 3F0TA 4IVPA 1P6XA 1E2MA 1OF1A 1E2JA 3VTKA
chains in the KnotProt database with same CATH homology

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