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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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

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