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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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
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3.1 8-156 149 1-7 285-310 157-284 7 26 slipknot
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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
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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
4JBYA 1KI7A 1P72A 1P75A 1KIMA 1KI8A 1KI6B 1P73A 1KI2A 4IVPA 1E2MA 1OSNA 1P6XA 1KI6A 1E2JA 2VTKA 3RDPA 1OF1A 1E2KA 1KI3A 1P7CA 1VTKA 1KI4A 1QHIA 2KI5A 1GKUB 1E2LA 1E2PA 1II9A 3VTKA 1E2HA 3F0TA 4JBXA 4IVQA 1F48A 1E2IA 1E2NA 4IVRA
chains in the KnotProt database with same CATH superfamily
4JBYA 1KI7A 1P72A 3FSGA 1P75A 1KIMA 1LNSA 1KI8A 3L04A 3L06A 1KI6B 1P73A 1KI2A 3KZOA 4IVPA 3M5CA 3KZMA 1E2MA 1OSNA 1R4NB 1QMGA 1P6XA 1KI6A 2XTJA 2FG6C 1E2JA 1JS1X 2VTKA 1OF1A 1E2KA 3RDPA 1KI3A 1P7CA 1VTKA 1KI4A 3KZNA 1QHIA 3FR7A 3KZCA 3FR8A 2G7MC 3M5DA 2KI5A 1GKUB 1E2LA 1E2PA 1YRLA 3M4JA 1E2HA 3L02A 3VTKA 1II9A 3M4NA 1YVEI 3KZKA 3F0TA 1DBIA 4JBXA 1R4MB 1YH1A 4IVQA 1F48A 3L05A 1E2IA 1E2NA 4IVRA
chains in the KnotProt database with same CATH topology
4JBYA 1KI7A 1P72A 1P75A 1KIMA 1KI8A 1KI6B 1P73A 1KI2A 4IVPA 1E2MA 1OSNA 1P6XA 1KI6A 1E2JA 2VTKA 3RDPA 1OF1A 1E2KA 1KI3A 1P7CA 1VTKA 1KI4A 1QHIA 2KI5A 1GKUB 1E2LA 1E2PA 1II9A 3VTKA 1E2HA 3F0TA 4JBXA 4IVQA 1F48A 1E2IA 1E2NA 4IVRA
chains in the KnotProt database with same CATH homology


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