1VTKA

Thymidine kinase from herpes simplex virus type 1 in complex with adp and deoxythymidine-monophosphate
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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: 119
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 5-117 113 1-4 304-331 118-303 4 28 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGS---PPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGPRP---------------HIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEAN
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 7-116 110 1-6 152-313 117-151 6 162 slipknot
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2.1 8-153 146 1-7 183-313 154-182 7 131 slipknot
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3.1 7-182 176 1-6 200-313 183-199 6 114 slipknot
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2.1 8-189 182 1-7 264-313 190-263 7 50 slipknot
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3.1 8-263 256 1-7 274-313 264-273 7 40 slipknot
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2.1 9-192 184 1-7, 260-313 8-8, 193-259 7 54 slipknot
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2.1 9-265 257 1-7, 274-313 8-8, 266-273 7 40 slipknot
sequence length 331
structure length 313
publication title The structures of thymidine kinase from herpes simplex virus type 1 in complex with substrates and a substrate analogue.
pubmed rcsb
molecule tags Transferase
molecule keywords THYMIDINE KINASE
source organism Herpes simplex virus (type 1 / strain f)
missing residues 105-107, 220-234
total genus Genus: 119
ec nomenclature ec 2.7.1.21: Thymidine kinase.
pdb deposition date 1997-04-01
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 1vtkA00
1QHIA 1P72A 1E2PA 1P7CA 1GKUB 1VTKA 1P75A 3VTKA 1KI6B 1P6XA 1E2MA 1F48A 1OF1A 1E2KA 1KI8A 4IVPA 1OSNA 1KIMA 1KI4A 1E2LA 3F0TA 3RDPA 1E2NA 1P73A 2VTKA 4IVRA 1KI3A 1KI6A 1E2HA 1KI2A 1II9A 4IVQA 4JBYA 2KI5A 4JBXA 1E2JA 1KI7A 1E2IA
chains in the KnotProt database with same CATH superfamily
1QHIA 1P72A 1E2PA 1P7CA 1GKUB 1VTKA 1P75A 3VTKA 1DBIA 3FSGA 3M4JA 1R4NB 3L02A 1KI6B 1P6XA 1E2MA 2G7MC 1YH1A 1F48A 1OF1A 3M5CA 3KZKA 1E2KA 3M5DA 3FR8A 1KI8A 3L04A 4IVPA 1OSNA 1JS1X 1KIMA 3L05A 1KI4A 1YVEI 2FG6C 1E2LA 1LNSA 3F0TA 3KZCA 3KZOA 1R4MB 3RDPA 1E2NA 3FR7A 1P73A 3KZNA 2VTKA 4IVRA 3KZMA 3M4NA 1KI3A 1QMGA 3L06A 1KI6A 1E2HA 1KI2A 1II9A 4IVQA 4JBYA 2KI5A 4JBXA 1E2JA 2XTJA 1KI7A 1E2IA 1YRLA
chains in the KnotProt database with same CATH topology
1QHIA 1P72A 1E2PA 1P7CA 1GKUB 1VTKA 1P75A 3VTKA 1KI6B 1P6XA 1E2MA 1F48A 1OF1A 1E2KA 1KI8A 4IVPA 1OSNA 1KIMA 1KI4A 1E2LA 3F0TA 3RDPA 1E2NA 1P73A 2VTKA 4IVRA 1KI3A 1KI6A 1E2HA 1KI2A 1II9A 4IVQA 4JBYA 2KI5A 4JBXA 1E2JA 1KI7A 1E2IA
chains in the KnotProt database with same CATH homology

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