1KIMA

Crystal structure of thymidine kinase from herpes simplex virus type i complexed with deoxythymidine
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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: 110
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 4-117 114 1-3 305-329 118-304 3 25 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKTTTTQLL-------DIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAPPALTLI------FDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSPRPHIGDTLFTLF----------------RAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
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 4-104 101 1-3 110-300 105-109 3 191 slipknot
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2.1 8-109 102 1-7 142-300 110-141 7 159 slipknot
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2.1 8-144 137 1-7 268-300 145-267 7 33 slipknot
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3.1 4-267 264 1-3 275-300 268-274 3 26 slipknot
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2.1 6-268 263 1-3, 275-300 4-5, 269-274 3 26 slipknot
sequence length 329
structure length 300
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 Transferase
molecule keywords THYMIDINE KINASE
source organism Herpes simplex virus (type 1 / strain 17)
missing residues 25-31, 103-108, 219-234
total genus Genus: 110
ec nomenclature ec 2.7.1.21: Thymidine kinase.
pdb deposition date 1997-11-12
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 1kimA00
1E2KA 1P72A 1KIMA 4JBYA 1E2HA 1E2JA 3F0TA 1KI7A 2VTKA 1GKUB 1E2MA 1OSNA 1QHIA 1E2IA 3RDPA 1E2PA 1KI6B 1VTKA 4JBXA 1P6XA 1OF1A 1KI2A 4IVPA 1KI4A 1P73A 3VTKA 1P75A 1KI3A 1KI6A 4IVRA 2KI5A 1F48A 1KI8A 1E2NA 1P7CA 1II9A 4IVQA 1E2LA
chains in the KnotProt database with same CATH superfamily
1E2KA 2G7MC 1P72A 3KZCA 1KIMA 4JBYA 1E2HA 1E2JA 3F0TA 1KI7A 3L06A 3KZNA 1JS1X 1YH1A 3KZMA 2VTKA 1GKUB 1E2MA 1YVEI 1OSNA 1QHIA 1E2IA 3FR8A 3RDPA 1E2PA 1KI6B 1VTKA 4JBXA 1P6XA 1R4NB 2XTJA 3KZKA 1OF1A 1KI2A 4IVPA 3FSGA 3L04A 1KI4A 1P73A 3L02A 3L05A 1P75A 3VTKA 1KI3A 1KI6A 1YRLA 3M4JA 4IVRA 1R4MB 2KI5A 1F48A 1KI8A 1LNSA 1E2NA 2FG6C 3M5CA 1DBIA 1QMGA 1P7CA 3KZOA 1II9A 3M5DA 3M4NA 4IVQA 3FR7A 1E2LA
chains in the KnotProt database with same CATH topology
1E2KA 1P72A 1KIMA 4JBYA 1E2HA 1E2JA 3F0TA 1KI7A 2VTKA 1GKUB 1E2MA 1OSNA 1QHIA 1E2IA 3RDPA 1E2PA 1KI6B 1VTKA 4JBXA 1P6XA 1OF1A 1KI2A 4IVPA 1KI4A 1P73A 3VTKA 1P75A 1KI3A 1KI6A 4IVRA 2KI5A 1F48A 1KI8A 1E2NA 1P7CA 1II9A 4IVQA 1E2LA
chains in the KnotProt database with same CATH homology

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