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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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

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