4IVPA

Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with in51/20
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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: 114
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
MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEA-----PPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGPRPHI---------------GDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
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 8-115 108 1-7 150-309 116-149 7 160 slipknot
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2.1 8-152 145 1-7 284-309 153-283 7 26 slipknot
sequence length 329
structure length 309
publication title New thymine derivatives as HSV1-TK ligand for the development of PET imaging tracer
rcsb
molecule tags Transferase
molecule keywords Thymidine kinase
source organism Human herpesvirus 1
missing residues 103-107, 220-234
total genus Genus: 114
ec nomenclature ec 2.7.1.21: Thymidine kinase.
pdb deposition date 2013-01-23
KnotProt deposition date 2014-08-19

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 4ivpA00
1OF1A 1E2KA 4IVQA 1E2MA 1P6XA 1KI2A 1F48A 1E2LA 2KI5A 1KI7A 1KI4A 1GKUB 1KI3A 3F0TA 4JBXA 4IVRA 1P72A 1E2JA 1VTKA 1E2NA 1KI8A 3RDPA 1P73A 1II9A 1E2HA 1E2IA 1P75A 3VTKA 2VTKA 1QHIA 4JBYA 1OSNA 1E2PA 4IVPA 1KI6B 1KI6A 1P7CA 1KIMA
chains in the KnotProt database with same CATH superfamily
1OF1A 1E2KA 4IVQA 1E2MA 3M5DA 1P6XA 3L06A 1R4MB 1KI2A 3L04A 1YVEI 1F48A 1E2LA 3L02A 3FR7A 2KI5A 3FSGA 1KI7A 1KI4A 1R4NB 1KI3A 3F0TA 1GKUB 4JBXA 4IVRA 1P72A 3KZMA 1E2JA 1VTKA 1E2NA 3KZNA 1YH1A 3FR8A 2FG6C 1KI8A 3RDPA 1P73A 1II9A 1E2HA 3M4NA 1DBIA 1E2IA 1P75A 2G7MC 3KZKA 3VTKA 1JS1X 3KZCA 3L05A 2VTKA 2XTJA 1QHIA 4JBYA 1QMGA 3KZOA 3M5CA 1OSNA 3M4JA 1E2PA 4IVPA 1KI6B 1KI6A 1P7CA 1LNSA 1YRLA 1KIMA
chains in the KnotProt database with same CATH topology
1OF1A 1E2KA 4IVQA 1E2MA 1P6XA 1KI2A 1F48A 1E2LA 2KI5A 1KI7A 1KI4A 1GKUB 1KI3A 3F0TA 4JBXA 4IVRA 1P72A 1E2JA 1VTKA 1E2NA 1KI8A 3RDPA 1P73A 1II9A 1E2HA 1E2IA 1P75A 3VTKA 2VTKA 1QHIA 4JBYA 1OSNA 1E2PA 4IVPA 1KI6B 1KI6A 1P7CA 1KIMA
chains in the KnotProt database with same CATH homology

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