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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Slipknot S +31
Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
+31 4-117 114 1-3 305-329 118-304 3 25 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKTTTTQLL-------DIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAPPALTLI------FDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSPRPHIGDTLFTLF----------------RAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
Whole chain analysis
Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1

Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
2.1 4-104 101 1-3 110-300 105-109 3 191 slipknot
view details
2.1 8-109 102 1-7 142-300 110-141 7 159 slipknot
view details
2.1 8-144 137 1-7 268-300 145-267 7 33 slipknot
view details
3.1 4-267 264 1-3 275-300 268-274 3 26 slipknot
view details
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
1II9A 1OSNA 4IVRA 1E2HA 1E2NA 1P7CA 4IVPA 1E2PA 1KI2A 1E2JA 3VTKA 1P73A 1QHIA 2VTKA 1E2KA 1P72A 1KI7A 1KI6B 4JBXA 1KI3A 1E2LA 1VTKA 2KI5A 4JBYA 4IVQA 1KIMA 1E2IA 1KI8A 1OF1A 1GKUB 1KI4A 3RDPA 1E2MA 1F48A 1P75A 1KI6A 1P6XA 3F0TA
chains in the KnotProt database with same CATH superfamily
1II9A 2G7MC 3L02A 1OSNA 4IVRA 1E2HA 1E2NA 1P7CA 3L04A 4IVPA 1E2PA 1KI2A 3FSGA 1YRLA 1E2JA 3VTKA 3FR8A 1P73A 1QHIA 2VTKA 1JS1X 1E2KA 1P72A 3M5CA 1KI7A 1KI6B 3M4NA 4JBXA 2FG6C 3M4JA 3KZKA 1YH1A 1DBIA 3FR7A 1YVEI 1KI3A 1E2LA 1LNSA 3KZOA 1VTKA 1QMGA 2KI5A 4JBYA 3KZNA 3L05A 1KIMA 4IVQA 3L06A 1R4NB 1E2IA 1KI8A 1OF1A 3KZCA 1GKUB 1KI4A 2XTJA 3M5DA 1R4MB 3RDPA 1E2MA 1F48A 1P75A 3KZMA 1KI6A 1P6XA 3F0TA
chains in the KnotProt database with same CATH topology
1II9A 1OSNA 4IVRA 1E2HA 1E2NA 1P7CA 4IVPA 1E2PA 1KI2A 1E2JA 3VTKA 1P73A 1QHIA 2VTKA 1E2KA 1P72A 1KI7A 1KI6B 4JBXA 1KI3A 1E2LA 1VTKA 2KI5A 4JBYA 4IVQA 1KIMA 1E2IA 1KI8A 1OF1A 1GKUB 1KI4A 3RDPA 1E2MA 1F48A 1P75A 1KI6A 1P6XA 3F0TA
chains in the KnotProt database with same CATH homology


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