4IVQA

Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with in43/5
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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: 109
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 4-117 114 1-3 306-329 118-305 3 24 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEA-----PPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRPGERL--DLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGPQSNAGP---------RPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
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 8-113 106 1-7 150-313 114-149 7 164 slipknot
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3.1 4-150 147 1-3 171-313 151-170 3 143 slipknot
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2.1 8-153 146 1-7 288-313 154-287 7 26 slipknot
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2.1 9-161 153 1-7, 277-313 8-8, 162-276 7 37 slipknot
sequence length 329
structure length 313
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, 176-177, 220-228
total genus Genus: 109
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 4ivqA00
1OSNA 3RDPA 1E2MA 1E2PA 2VTKA 1E2NA 1E2IA 1E2HA 3F0TA 1GKUB 1VTKA 1QHIA 1KI6B 1P75A 2KI5A 1P73A 1KI3A 1E2KA 4JBYA 1OF1A 1KI6A 1F48A 1KI7A 1P6XA 1P72A 1KIMA 1II9A 1KI2A 1E2LA 1E2JA 1KI4A 4IVPA 3VTKA 1KI8A 4IVRA 4IVQA 4JBXA 1P7CA
chains in the KnotProt database with same CATH superfamily
1OSNA 1QMGA 3RDPA 3KZCA 1E2MA 1E2PA 2VTKA 3FR7A 3KZNA 1R4NB 3L06A 2FG6C 1LNSA 1E2NA 1E2IA 1E2HA 3L02A 3F0TA 1GKUB 1VTKA 1YH1A 3M5DA 1YVEI 1QHIA 1KI6B 1P75A 2KI5A 1P73A 1KI3A 3KZKA 1E2KA 3M4JA 4JBYA 1OF1A 1KI6A 1F48A 3L04A 1KI7A 3M4NA 1P6XA 1P72A 1KIMA 2XTJA 1II9A 1YRLA 3FR8A 1KI2A 1E2LA 3M5CA 1DBIA 3KZMA 1E2JA 3L05A 1KI4A 2G7MC 3FSGA 4IVPA 1JS1X 3VTKA 1KI8A 4IVRA 4IVQA 3KZOA 4JBXA 1P7CA 1R4MB
chains in the KnotProt database with same CATH topology
1OSNA 3RDPA 1E2MA 1E2PA 2VTKA 1E2NA 1E2IA 1E2HA 3F0TA 1GKUB 1VTKA 1QHIA 1KI6B 1P75A 2KI5A 1P73A 1KI3A 1E2KA 4JBYA 1OF1A 1KI6A 1F48A 1KI7A 1P6XA 1P72A 1KIMA 1II9A 1KI2A 1E2LA 1E2JA 1KI4A 4IVPA 3VTKA 1KI8A 4IVRA 4IVQA 4JBXA 1P7CA
chains in the KnotProt database with same CATH homology

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