1OF1A

Kinetics and crystal structure of the herpes simplex virus type 1 thymidine kinase interacting with (south)-methanocarba-thymidine
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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: 111
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 5-117 113 1-4 305-329 118-304 4 25 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKTTTTQLLVA----DDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAPPPA-----LTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTGPRPHIGDT-------------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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2.1 8-108 101 1-7 147-307 109-146 7 161 slipknot
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2.1 9-147 139 1-8 281-307 148-280 8 27 slipknot
sequence length 329
structure length 307
publication title Biochemical and Structural Characterization of (South)-Methanocarbathymidine that Specifically Inhibits Growth of Herpes Simplex Virus Type 1 Thymidine Kinase-Transduced Osteosarcoma Cells
pubmed doi rcsb
molecule tags Transferase
molecule keywords THYMIDINE KINASE
source organism Herpes simplex virus (type 1 / strain 17)
missing residues 27-30, 103-107, 221-233
total genus Genus: 111
ec nomenclature ec 2.7.1.21: Thymidine kinase.
pdb deposition date 2003-04-03
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 1of1A00
1KI6B 1F48A 2KI5A 1E2PA 4IVPA 1P73A 1VTKA 1E2HA 1OSNA 3VTKA 4JBYA 4IVRA 1E2IA 3F0TA 1P72A 1E2LA 4JBXA 1P75A 4IVQA 1KI6A 1OF1A 1KI8A 1KI3A 1E2MA 1E2KA 1KI7A 1KI2A 1P7CA 1E2JA 1P6XA 1GKUB 1E2NA 2VTKA 3RDPA 1QHIA 1II9A 1KI4A 1KIMA
chains in the KnotProt database with same CATH superfamily
1KI6B 3FR8A 3KZNA 3M4NA 1YRLA 1F48A 2FG6C 3M4JA 2KI5A 1R4MB 1E2PA 1LNSA 1P73A 1VTKA 4IVPA 3KZMA 1DBIA 3L04A 1E2HA 1OSNA 1JS1X 3VTKA 4JBYA 1E2IA 4IVRA 3F0TA 1P72A 1E2LA 4JBXA 3L02A 1P75A 3L05A 4IVQA 1KI6A 2G7MC 3KZOA 1OF1A 3FSGA 1KI8A 1KI3A 1R4NB 1E2MA 1YH1A 3M5CA 1E2KA 3FR7A 1KI7A 1YVEI 1KI2A 3KZKA 1P7CA 1QMGA 1E2JA 1P6XA 2XTJA 3M5DA 1E2NA 2VTKA 3L06A 3KZCA 3RDPA 1GKUB 1QHIA 1II9A 1KI4A 1KIMA
chains in the KnotProt database with same CATH topology
1KI6B 1F48A 2KI5A 1E2PA 4IVPA 1P73A 1VTKA 1E2HA 1OSNA 3VTKA 4JBYA 4IVRA 1E2IA 3F0TA 1P72A 1E2LA 4JBXA 1P75A 4IVQA 1KI6A 1OF1A 1KI8A 1KI3A 1E2MA 1E2KA 1KI7A 1KI2A 1P7CA 1E2JA 1P6XA 1GKUB 1E2NA 2VTKA 3RDPA 1QHIA 1II9A 1KI4A 1KIMA
chains in the KnotProt database with same CATH homology

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