4JBYA

Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with f-sk78
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 1-5 306-330 119-305 5 25 slipknot
Chain Sequence
KMPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEA-----PPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGPRPHI---------------GDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
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 8-125 118 1-7 150-310 126-149 7 161 slipknot
view details
3.1 8-149 142 1-7 151-310 150-150 7 160 slipknot
view details
3.1 8-156 149 1-7 285-310 157-284 7 26 slipknot
view details
2.1 8-116 109 1-2, 126-310 3-7, 117-125 2 185 slipknot
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2.1 9-133 125 1-7, 150-310 8-8, 134-149 7 161 slipknot
view details
2.1 9-156 148 1-7, 280-310 8-8, 157-279 7 31 slipknot
view details
2.1 10-162 153 1-8, 275-310 9-9, 163-274 8 36 slipknot
sequence length 330
structure length 310
publication title New thymine derivatives as HSV1-TK ligand for the development of PET imaging tracer
rcsb
molecule tags Transferase
molecule keywords Thymidine kinase
source organism Human herpesvirus 1
missing residues 104-108, 221-235
total genus Genus: 114
ec nomenclature ec 2.7.1.21: Thymidine kinase.
pdb deposition date 2013-02-20
KnotProt deposition date 2014-08-19

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 4jbyA00
1II9A 1P6XA 1KI2A 1E2IA 1E2NA 1KI3A 1KIMA 1KI6A 1GKUB 1E2JA 1E2HA 1OF1A 4IVRA 3RDPA 1OSNA 1E2PA 1KI4A 1KI7A 2VTKA 1KI6B 1VTKA 1P75A 1E2KA 3VTKA 3F0TA 4IVPA 1KI8A 1QHIA 1P73A 4IVQA 1E2MA 4JBYA 1P7CA 1P72A 4JBXA 1E2LA 2KI5A 1F48A
chains in the KnotProt database with same CATH superfamily
1II9A 1P6XA 1KI2A 1YH1A 1E2IA 1E2NA 1KI3A 1JS1X 1KI6A 1KIMA 1R4NB 1GKUB 1E2JA 3L06A 1YVEI 2XTJA 1E2HA 2FG6C 1OF1A 3KZMA 1DBIA 4IVRA 3L02A 3RDPA 1OSNA 1E2PA 2G7MC 3L05A 1KI4A 3M4NA 1KI7A 2VTKA 1KI6B 1VTKA 3KZKA 1P75A 1E2KA 3VTKA 1YRLA 3F0TA 4IVPA 1KI8A 1QHIA 3FR7A 1P73A 4IVQA 3FR8A 1E2MA 3KZOA 1QMGA 4JBYA 3M5DA 1P7CA 3KZNA 3M4JA 1R4MB 3KZCA 1P72A 3L04A 1LNSA 3M5CA 1E2LA 2KI5A 4JBXA 1F48A 3FSGA
chains in the KnotProt database with same CATH topology
1II9A 1P6XA 1KI2A 1E2IA 1E2NA 1KI3A 1KIMA 1KI6A 1GKUB 1E2JA 1E2HA 1OF1A 4IVRA 3RDPA 1OSNA 1E2PA 1KI4A 1KI7A 2VTKA 1KI6B 1VTKA 1P75A 1E2KA 3VTKA 3F0TA 4IVPA 1KI8A 1QHIA 1P73A 4IVQA 1E2MA 4JBYA 1P7CA 1P72A 4JBXA 1E2LA 2KI5A 1F48A
chains in the KnotProt database with same CATH homology


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