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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Genus: 108
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 4-116 113 1-3 306-329 117-305 3 24 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKTTTTQLLVAL----DIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAPPAL------TLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLAGPRPHIGDT---------------LFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
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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3.1 7-117 111 1-6 145-304 118-144 6 160 slipknot
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3.1 4-147 144 1-3 164-304 148-163 3 141 slipknot
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2.1 9-148 140 1-8 279-304 149-278 8 26 slipknot
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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
4JBYA 2KI5A 1E2LA 1P72A 1OF1A 1E2JA 1F48A 1VTKA 1KI6B 3VTKA 1P7CA 1KI7A 3RDPA 4IVRA 2VTKA 1E2MA 1II9A 1KI4A 1OSNA 4IVQA 4JBXA 1E2NA 1KI6A 1KI8A 1P75A 3F0TA 1KIMA 1GKUB 1E2PA 1QHIA 1P6XA 1E2HA 1E2KA 1KI3A 4IVPA 1KI2A 1P73A 1E2IA
chains in the KnotProt database with same CATH superfamily
3L02A 4JBYA 2KI5A 1E2LA 1P72A 3L05A 1OF1A 1E2JA 1F48A 3FR7A 1YVEI 3M4NA 1VTKA 1KI6B 3FR8A 3M5CA 3VTKA 1P7CA 3L04A 3KZOA 1KI7A 3FSGA 3M4JA 3RDPA 4IVRA 2VTKA 2G7MC 1E2MA 3M5DA 1LNSA 1II9A 1KI4A 2XTJA 1OSNA 4IVQA 1DBIA 4JBXA 1E2NA 1KI6A 1KI8A 1P75A 3F0TA 3KZNA 3L06A 1KIMA 3KZKA 3KZMA 1E2PA 1YH1A 1QHIA 1P6XA 1E2HA 1GKUB 1JS1X 1E2KA 1YRLA 1KI3A 4IVPA 1R4NB 1KI2A 1P73A 1QMGA 2FG6C 3KZCA 1R4MB 1E2IA
chains in the KnotProt database with same CATH topology
4JBYA 2KI5A 1E2LA 1P72A 1OF1A 1E2JA 1F48A 1VTKA 1KI6B 3VTKA 1P7CA 1KI7A 3RDPA 4IVRA 2VTKA 1E2MA 1II9A 1KI4A 1OSNA 4IVQA 4JBXA 1E2NA 1KI6A 1KI8A 1P75A 3F0TA 1KIMA 1GKUB 1E2PA 1QHIA 1P6XA 1E2HA 1E2KA 1KI3A 4IVPA 1KI2A 1P73A 1E2IA
chains in the KnotProt database with same CATH homology

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