1KI7A

Crystal structure of thymidine kinase from herpes simplex virus type i complexed with 5-iododeoxyuridine
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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: 103
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 1-4 305-329 118-304 4 25 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKTTTTQLL-------DIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSAPPPALT--LIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQPRPHIGDTL------------------FTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
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 7-109 103 1-6 124-302 110-123 6 179 slipknot
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2.1 8-115 108 1-7 174-302 116-173 7 129 slipknot
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2.1 8-174 167 1-7 256-302 175-255 7 47 slipknot
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3.1 6-256 251 1-5 277-302 257-276 5 26 slipknot
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3.1 4-276 273 1-3 278-302 277-277 3 25 slipknot
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2.1 9-198 190 1-7, 250-302 8-8, 199-249 7 53 slipknot
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2.1 8-256 249 1-5, 275-302 6-7, 257-274 5 28 slipknot
sequence length 329
structure length 302
publication title Exploring the active site of herpes simplex virus type-1 thymidine kinase by X-ray crystallography of complexes with aciclovir and other ligands.
pubmed doi rcsb
molecule tags Phosphotransferase
molecule keywords THYMIDINE KINASE
source organism Herpes simplex virus (type 1 / strain 17)
missing residues 25-31, 105-106, 217-234
total genus Genus: 103
ec nomenclature ec 2.7.1.21: Thymidine kinase.
pdb deposition date 1998-05-15
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 1ki7A00
3F0TA 1E2IA 1F48A 1P6XA 1KI6B 1KI7A 2KI5A 1E2HA 4JBXA 1OF1A 1P72A 3RDPA 1E2JA 1E2MA 1II9A 1KI8A 1OSNA 1KI3A 4IVRA 1P7CA 1VTKA 4JBYA 2VTKA 4IVQA 1KI2A 1P73A 1QHIA 1E2LA 1E2KA 1E2PA 1KI6A 1P75A 4IVPA 1KIMA 1E2NA 3VTKA 1GKUB 1KI4A
chains in the KnotProt database with same CATH superfamily
3F0TA 3FR8A 1E2IA 1F48A 1P6XA 2XTJA 1YRLA 3KZKA 1DBIA 3KZOA 1KI6B 2G7MC 1KI7A 2KI5A 3L02A 3FR7A 3L06A 3M4JA 1E2HA 3KZNA 4JBXA 1OF1A 1P72A 3RDPA 3L05A 1R4MB 1E2JA 3KZCA 1E2MA 1II9A 3L04A 1KI8A 1OSNA 1KI3A 4IVRA 1P7CA 1VTKA 3M4NA 4JBYA 2VTKA 4IVQA 1KI2A 1P73A 2FG6C 3KZMA 1QHIA 1E2LA 3M5CA 1LNSA 1R4NB 1E2KA 1E2PA 1KI6A 1P75A 1YVEI 3FSGA 1YH1A 4IVPA 1KIMA 1E2NA 3M5DA 3VTKA 1QMGA 1GKUB 1KI4A 1JS1X
chains in the KnotProt database with same CATH topology
3F0TA 1E2IA 1F48A 1P6XA 1KI6B 1KI7A 2KI5A 1E2HA 4JBXA 1OF1A 1P72A 3RDPA 1E2JA 1E2MA 1II9A 1KI8A 1OSNA 1KI3A 4IVRA 1P7CA 1VTKA 4JBYA 2VTKA 4IVQA 1KI2A 1P73A 1QHIA 1E2LA 1E2KA 1E2PA 1KI6A 1P75A 4IVPA 1KIMA 1E2NA 3VTKA 1GKUB 1KI4A
chains in the KnotProt database with same CATH homology

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