4JBXA

Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with sk-78
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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: 113
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 6-117 112 1-5 307-330 118-306 5 24 slipknot
Chain Sequence
KMPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEA-----PPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGPRPHI---------------GDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
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 9-116 108 1-8 152-310 117-151 8 159 slipknot
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3.1 5-151 147 1-4 155-310 152-154 4 156 slipknot
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3.1 9-152 144 1-8 279-310 153-278 8 32 slipknot
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3.1 5-278 274 1-4 284-310 279-283 4 27 slipknot
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3.1 5-283 279 1-4 285-310 284-284 4 26 slipknot
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3.1 7-279 273 1-4, 285-310 5-6, 280-284 4 26 slipknot
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2.1 10-165 156 1-8, 276-310 9-9, 166-275 8 35 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: 113
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 4jbxA00
1P73A 1E2NA 1F48A 1OF1A 3RDPA 1E2IA 1KI6A 1GKUB 1KI8A 1P72A 1KI6B 1E2PA 1E2JA 3F0TA 1KI2A 3VTKA 1E2MA 2KI5A 4JBYA 1KIMA 4IVPA 2VTKA 1KI7A 1VTKA 1OSNA 1P6XA 1E2KA 1KI4A 1II9A 1E2HA 1E2LA 4IVRA 1P75A 1KI3A 4IVQA 4JBXA 1QHIA 1P7CA
chains in the KnotProt database with same CATH superfamily
1P73A 2G7MC 1R4NB 3KZOA 1E2NA 1F48A 1OF1A 3M5CA 3RDPA 1DBIA 1E2IA 1KI6A 3M4NA 1GKUB 1KI8A 1P72A 1KI6B 1JS1X 1E2PA 1E2JA 3F0TA 1YRLA 2XTJA 2FG6C 3KZNA 1KI2A 1YVEI 3VTKA 1E2MA 2KI5A 3KZCA 4JBYA 1KIMA 4IVPA 3FSGA 2VTKA 3M5DA 3KZMA 1KI7A 1VTKA 1R4MB 1OSNA 1E2KA 1KI4A 1P6XA 3L06A 3KZKA 3FR8A 1II9A 1LNSA 1E2HA 1YH1A 3M4JA 3L04A 1E2LA 3L02A 3L05A 4IVRA 1P75A 1KI3A 3FR7A 1QMGA 4IVQA 4JBXA 1QHIA 1P7CA
chains in the KnotProt database with same CATH topology
1P73A 1E2NA 1F48A 1OF1A 3RDPA 1E2IA 1KI6A 1GKUB 1KI8A 1P72A 1KI6B 1E2PA 1E2JA 3F0TA 1KI2A 3VTKA 1E2MA 2KI5A 4JBYA 1KIMA 4IVPA 2VTKA 1KI7A 1VTKA 1OSNA 1P6XA 1E2KA 1KI4A 1II9A 1E2HA 1E2LA 4IVRA 1P75A 1KI3A 4IVQA 4JBXA 1QHIA 1P7CA
chains in the KnotProt database with same CATH homology

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