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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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
4IVRA 1OF1A 1KI7A 2KI5A 1E2KA 1E2LA 3F0TA 4JBYA 4IVQA 1E2MA 1KIMA 1KI6B 1II9A 1VTKA 1GKUB 1P72A 4JBXA 1KI3A 1P7CA 1KI8A 1E2JA 1E2NA 1KI6A 1OSNA 1KI4A 1QHIA 1P6XA 1P73A 4IVPA 2VTKA 1KI2A 1E2HA 1E2IA 3VTKA 1E2PA 1P75A 1F48A 3RDPA
chains in the KnotProt database with same CATH superfamily
4IVRA 1OF1A 3KZNA 1QMGA 1YH1A 1KI7A 3KZOA 2FG7C 3FR7A 2KI5A 2FG7X 3KZMA 1YRLA 1E2KA 1E2LA 3F0TA 3M5DA 4JBYA 4IVQA 1E2MA 1KIMA 1KI6B 1II9A 1VTKA 1GKUB 1P72A 3M4NA 4JBXA 1R4NB 1KI3A 3M5CA 1JS1X 1P7CA 3L02A 1KI8A 1LNSA 3L05A 1E2JA 1E2NA 1KI6A 3M4JA 1OSNA 1R4MB 2XTJA 3L04A 1KI4A 1QHIA 1P6XA 1P73A 3FSGA 2VTKA 1KI2A 3KZCA 1E2HA 4IVPA 1YVEI 1E2IA 3VTKA 3FR8A 2G7MC 2FG6C 1DBIA 1E2PA 1P75A 1F48A 3L06A 3KZKA 3RDPA
chains in the KnotProt database with same CATH topology
4IVRA 1OF1A 1KI7A 2KI5A 1E2KA 1E2LA 3F0TA 4JBYA 4IVQA 1E2MA 1KIMA 1KI6B 1II9A 1VTKA 1GKUB 1P72A 4JBXA 1KI3A 1P7CA 1KI8A 1E2JA 1E2NA 1KI6A 1OSNA 1KI4A 1QHIA 1P6XA 1P73A 4IVPA 2VTKA 1KI2A 1E2HA 1E2IA 3VTKA 1E2PA 1P75A 1F48A 3RDPA
chains in the KnotProt database with same CATH homology


 
#chains in the KnotProt database with same CATH superfamily
 4IVR A;  1OF1 A;  1KI7 A;  2KI5 A;  1E2K A;  1E2L A;  3F0T A;  4JBY A;  4IVQ A;  1E2M A;  1KIM A;  1KI6 B;  1II9 A;  1VTK A;  1GKU B;  1P72 A;  4JBX A;  1KI3 A;  1P7C A;  1KI8 A;  1E2J A;  1E2N A;  1KI6 A;  1OSN A;  1KI4 A;  1QHI A;  1P6X A;  1P73 A;  4IVP A;  2VTK A;  1KI2 A;  1E2H A;  1E2I A;  3VTK A;  1E2P A;  1P75 A;  1F48 A;  3RDP A; 
#chains in the KnotProt database with same CATH topology
 4IVR A;  1OF1 A;  3KZN A;  1QMG A;  1YH1 A;  1KI7 A;  3KZO A;  2FG7 C;  3FR7 A;  2KI5 A;  2FG7 X;  3KZM A;  1YRL A;  1E2K A;  1E2L A;  3F0T A;  3M5D A;  4JBY A;  4IVQ A;  1E2M A;  1KIM A;  1KI6 B;  1II9 A;  1VTK A;  1GKU B;  1P72 A;  3M4N A;  4JBX A;  1R4N B;  1KI3 A;  3M5C A;  1JS1 X;  1P7C A;  3L02 A;  1KI8 A;  1LNS A;  3L05 A;  1E2J A;  1E2N A;  1KI6 A;  3M4J A;  1OSN A;  1R4M B;  2XTJ A;  3L04 A;  1KI4 A;  1QHI A;  1P6X A;  1P73 A;  3FSG A;  2VTK A;  1KI2 A;  3KZC A;  1E2H A;  4IVP A;  1YVE I;  1E2I A;  3VTK A;  3FR8 A;  2G7M C;  2FG6 C;  1DBI A;  1E2P A;  1P75 A;  1F48 A;  3L06 A;  3KZK A;  3RDP A; 
#chains in the KnotProt database with same CATH homology
 4IVR A;  1OF1 A;  1KI7 A;  2KI5 A;  1E2K A;  1E2L A;  3F0T A;  4JBY A;  4IVQ A;  1E2M A;  1KIM A;  1KI6 B;  1II9 A;  1VTK A;  1GKU B;  1P72 A;  4JBX A;  1KI3 A;  1P7C A;  1KI8 A;  1E2J A;  1E2N A;  1KI6 A;  1OSN A;  1KI4 A;  1QHI A;  1P6X A;  1P73 A;  4IVP A;  2VTK A;  1KI2 A;  1E2H A;  1E2I A;  3VTK A;  1E2P A;  1P75 A;  1F48 A;  3RDP 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)

 
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#similar chains, but unknotted
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