1KI6B

Crystal structure of thymidine kinase from herpes simplex virus type i complexed with a 5-iodouracil anhydrohexitol nucleoside
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 4-116 113 1-3 306-329 117-305 3 24 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKTTTTQLLVAL----DIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAPPAL------TLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLAGPRPHIGDT---------------LFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
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
3.1 7-117 111 1-6 145-304 118-144 6 160 slipknot
view details
3.1 4-147 144 1-3 164-304 148-163 3 141 slipknot
view details
2.1 9-148 140 1-8 279-304 149-278 8 26 slipknot
view details
2.1 6-146 141 1-2, 149-304 3-5, 147-148 2 156 slipknot
sequence length 329
structure length 304
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 28-31, 103-108, 218-232
total genus Genus: 108
ec nomenclature ec 2.7.1.21: Thymidine kinase.
pdb deposition date 1998-05-18
KnotProt deposition date 2014-10-08

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
B PF00693 Herpes_TK Thymidine kinase from herpesvirus
B PF00693.13 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 1ki6B00
1E2MA 4JBYA 1E2JA 4IVQA 3F0TA 1E2PA 1P73A 1P75A 3RDPA 1E2NA 1VTKA 3VTKA 1GKUB 1F48A 4IVRA 1QHIA 2VTKA 1KI4A 1KI8A 1OF1A 1KI6B 1II9A 1P7CA 2KI5A 1E2LA 1P6XA 1E2HA 1E2KA 4IVPA 1KI3A 1E2IA 1KI7A 1KIMA 4JBXA 1OSNA 1P72A 1KI2A 1KI6A
chains in the KnotProt database with same CATH superfamily
1QMGA 2XTJA 1E2MA 4JBYA 1E2JA 3KZNA 4IVQA 1YH1A 3F0TA 1DBIA 1E2PA 1P73A 1P75A 3L05A 1R4NB 2FG7C 3RDPA 1E2NA 1VTKA 3FR7A 3VTKA 1GKUB 1F48A 3KZMA 4IVRA 1JS1X 1QHIA 3FSGA 2VTKA 1KI4A 3L04A 3M4JA 1KI8A 1OF1A 1YRLA 2FG6C 1KI6B 1II9A 2FG7X 3KZKA 3L06A 3KZOA 1P7CA 2KI5A 3KZCA 1E2LA 1E2HA 1P6XA 1LNSA 1E2KA 4IVPA 3M5CA 3FR8A 1KI3A 1YVEI 2G7MC 1E2IA 1KI7A 1KIMA 3L02A 3M5DA 3M4NA 1OSNA 4JBXA 1P72A 1R4MB 1KI2A 1KI6A
chains in the KnotProt database with same CATH topology
1E2MA 4JBYA 1E2JA 4IVQA 3F0TA 1E2PA 1P73A 1P75A 3RDPA 1E2NA 1VTKA 3VTKA 1GKUB 1F48A 4IVRA 1QHIA 2VTKA 1KI4A 1KI8A 1OF1A 1KI6B 1II9A 1P7CA 2KI5A 1E2LA 1P6XA 1E2HA 1E2KA 4IVPA 1KI3A 1E2IA 1KI7A 1KIMA 4JBXA 1OSNA 1P72A 1KI2A 1KI6A
chains in the KnotProt database with same CATH homology


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

 
#similar chains in the KnotProt database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...

KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling