3VTKA

Thymidine kinase from herpes simplex virus type 1 in complex with adp and 5-iodo-deoxyuridine-monophosphate
Warning
  • Chain breaks within knotoid 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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
  • 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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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: 97
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 5-118 114 1-4 305-331 119-304 4 27 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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3.1 7-116 110 1-6 152-313 117-151 6 162 slipknot
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3.1 4-157 154 1-3 186-313 158-185 3 128 slipknot
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2.1 8-158 151 1-7 262-313 159-261 7 52 slipknot
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3.1 4-261 258 1-3 271-313 262-270 3 43 slipknot
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3.1 6-262 257 1-5 283-313 263-282 5 31 slipknot
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2.1 9-162 154 1-7, 252-313 8-8, 163-251 7 62 slipknot
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2.1 8-263 256 1-5, 283-313 6-7, 264-282 5 31 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: 97
ec nomenclature ec 2.7.1.21: Thymidine kinase.
pdb deposition date 1997-04-01
KnotProt deposition date 2014-07-31
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 3vtkA00
3RDPA 1E2HA 1VTKA 1KI8A 1E2JA 1P7CA 1KIMA 3F0TA 1E2PA 1KI6A 4IVRA 1KI3A 1P72A 1E2NA 1P73A 1E2IA 1GKUB 4JBXA 1KI6B 1E2LA 1E2MA 1KI7A 2VTKA 1P75A 2KI5A 4JBYA 4IVQA 1E2KA 1OF1A 1II9A 1KI4A 1KI2A 1P6XA 4IVPA 1QHIA 1OSNA 3VTKA 1F48A
chains in the KnotProt database with same CATH superfamily
3RDPA 3L04A 1E2HA 1VTKA 1YRLA 3L02A 3M5CA 1KI8A 2XTJA 1E2JA 2G7MC 1P7CA 1KIMA 1YVEI 3F0TA 1E2PA 1KI6A 4IVRA 1KI3A 1P72A 3KZNA 3M5DA 1E2NA 1P73A 1R4MB 1JS1X 3FR7A 3KZMA 1E2IA 1GKUB 3KZOA 4JBXA 1KI6B 1E2LA 1E2MA 1KI7A 2VTKA 1P75A 3L06A 2KI5A 1YH1A 3FR8A 3M4NA 4JBYA 4IVQA 1E2KA 1OF1A 3M4JA 1II9A 1KI4A 1KI2A 1P6XA 1R4NB 1QMGA 4IVPA 3L05A 1QHIA 2FG6C 3KZCA 3KZKA 1OSNA 1DBIA 1LNSA 3FSGA 3VTKA 1F48A
chains in the KnotProt database with same CATH topology
3RDPA 1E2HA 1VTKA 1KI8A 1E2JA 1P7CA 1KIMA 3F0TA 1E2PA 1KI6A 4IVRA 1KI3A 1P72A 1E2NA 1P73A 1E2IA 1GKUB 4JBXA 1KI6B 1E2LA 1E2MA 1KI7A 2VTKA 1P75A 2KI5A 4JBYA 4IVQA 1E2KA 1OF1A 1II9A 1KI4A 1KI2A 1P6XA 4IVPA 1QHIA 1OSNA 3VTKA 1F48A
chains in the KnotProt database with same CATH homology

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