1KI2A

Crystal structure of thymidine kinase from herpes simplex virus type i complexed with ganciclovir
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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: 101
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
MPTLLRVYIDGPHGMGKTTTTQLLVA-----DIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQPRPHI------------------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 8-129 122 1-7 168-306 130-167 7 139 slipknot
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3.1 4-167 164 1-3 223-306 168-222 3 84 slipknot
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2.1 8-168 161 1-7 281-306 169-280 7 26 slipknot
sequence length 329
structure length 306
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 27-31, 217-234
total genus Genus: 101
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 1ki2A00
4IVPA 4JBYA 1P7CA 1KI8A 1F48A 1KI3A 1P73A 4IVQA 1OSNA 2VTKA 3RDPA 1KI2A 1II9A 3F0TA 1P72A 1KI6B 1E2JA 1KI4A 1P6XA 1P75A 3VTKA 1GKUB 1E2KA 2KI5A 1E2IA 1E2PA 1KIMA 1E2MA 1OF1A 1E2NA 4IVRA 4JBXA 1KI7A 1VTKA 1E2HA 1QHIA 1E2LA 1KI6A
chains in the KnotProt database with same CATH superfamily
4IVPA 3M4JA 4JBYA 1P7CA 1LNSA 1KI8A 3L05A 1F48A 1KI3A 3FR8A 1P73A 1JS1X 4IVQA 3KZMA 1OSNA 1DBIA 2VTKA 3FR7A 3RDPA 1KI2A 3KZNA 1II9A 1YRLA 3F0TA 1YH1A 1P72A 1KI6B 3L06A 1E2JA 1KI4A 1P6XA 3KZCA 1QMGA 1P75A 3VTKA 1R4MB 1E2KA 1GKUB 1YVEI 3M4NA 3L04A 2XTJA 1R4NB 2KI5A 3L02A 3M5CA 1E2IA 2G7MC 1E2PA 1KIMA 3KZKA 3FSGA 3M5DA 1E2MA 1OF1A 1E2NA 3KZOA 4IVRA 4JBXA 1KI7A 1VTKA 1E2HA 1QHIA 2FG6C 1E2LA 1KI6A
chains in the KnotProt database with same CATH topology
4IVPA 4JBYA 1P7CA 1KI8A 1F48A 1KI3A 1P73A 4IVQA 1OSNA 2VTKA 3RDPA 1KI2A 1II9A 3F0TA 1P72A 1KI6B 1E2JA 1KI4A 1P6XA 1P75A 3VTKA 1GKUB 1E2KA 2KI5A 1E2IA 1E2PA 1KIMA 1E2MA 1OF1A 1E2NA 4IVRA 4JBXA 1KI7A 1VTKA 1E2HA 1QHIA 1E2LA 1KI6A
chains in the KnotProt database with same CATH homology

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