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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Slipknot S +31
Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
+31 4-117 114 1-3 306-329 118-305 3 24 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEA-----PPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRPGERL--DLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGPQSNAGP---------RPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
Whole chain analysis
Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1

Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
2.1 8-113 106 1-7 150-313 114-149 7 164 slipknot
view details
3.1 4-150 147 1-3 171-313 151-170 3 143 slipknot
view details
2.1 8-153 146 1-7 288-313 154-287 7 26 slipknot
view details
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
4IVRA 1OF1A 1KI7A 2KI5A 1E2KA 1E2LA 3F0TA 4JBYA 4IVQA 1E2MA 1KIMA 1KI6B 1II9A 1VTKA 1GKUB 1P72A 4JBXA 1KI3A 1P7CA 1KI8A 1E2JA 1E2NA 1KI6A 1OSNA 1KI4A 1QHIA 1P6XA 1P73A 4IVPA 2VTKA 1KI2A 1E2HA 1E2IA 3VTKA 1E2PA 1P75A 1F48A 3RDPA
chains in the KnotProt database with same CATH superfamily
4IVRA 1OF1A 3KZNA 1QMGA 1YH1A 1KI7A 3KZOA 2FG7C 3FR7A 2KI5A 2FG7X 3KZMA 1YRLA 1E2KA 1E2LA 3F0TA 3M5DA 4JBYA 4IVQA 1E2MA 1KIMA 1KI6B 1II9A 1VTKA 1GKUB 1P72A 3M4NA 4JBXA 1R4NB 1KI3A 3M5CA 1JS1X 1P7CA 3L02A 1KI8A 1LNSA 3L05A 1E2JA 1E2NA 1KI6A 3M4JA 1OSNA 1R4MB 2XTJA 3L04A 1KI4A 1QHIA 1P6XA 1P73A 3FSGA 2VTKA 1KI2A 3KZCA 1E2HA 4IVPA 1YVEI 1E2IA 3VTKA 3FR8A 2G7MC 2FG6C 1DBIA 1E2PA 1P75A 1F48A 3L06A 3KZKA 3RDPA
chains in the KnotProt database with same CATH topology
4IVRA 1OF1A 1KI7A 2KI5A 1E2KA 1E2LA 3F0TA 4JBYA 4IVQA 1E2MA 1KIMA 1KI6B 1II9A 1VTKA 1GKUB 1P72A 4JBXA 1KI3A 1P7CA 1KI8A 1E2JA 1E2NA 1KI6A 1OSNA 1KI4A 1QHIA 1P6XA 1P73A 4IVPA 2VTKA 1KI2A 1E2HA 1E2IA 3VTKA 1E2PA 1P75A 1F48A 3RDPA
chains in the KnotProt database with same CATH homology


 
#chains in the KnotProt database with same CATH superfamily
 4IVR A;  1OF1 A;  1KI7 A;  2KI5 A;  1E2K A;  1E2L A;  3F0T A;  4JBY A;  4IVQ A;  1E2M A;  1KIM A;  1KI6 B;  1II9 A;  1VTK A;  1GKU B;  1P72 A;  4JBX A;  1KI3 A;  1P7C A;  1KI8 A;  1E2J A;  1E2N A;  1KI6 A;  1OSN A;  1KI4 A;  1QHI A;  1P6X A;  1P73 A;  4IVP A;  2VTK A;  1KI2 A;  1E2H A;  1E2I A;  3VTK A;  1E2P A;  1P75 A;  1F48 A;  3RDP A; 
#chains in the KnotProt database with same CATH topology
 4IVR A;  1OF1 A;  3KZN A;  1QMG A;  1YH1 A;  1KI7 A;  3KZO A;  2FG7 C;  3FR7 A;  2KI5 A;  2FG7 X;  3KZM A;  1YRL A;  1E2K A;  1E2L A;  3F0T A;  3M5D A;  4JBY A;  4IVQ A;  1E2M A;  1KIM A;  1KI6 B;  1II9 A;  1VTK A;  1GKU B;  1P72 A;  3M4N A;  4JBX A;  1R4N B;  1KI3 A;  3M5C A;  1JS1 X;  1P7C A;  3L02 A;  1KI8 A;  1LNS A;  3L05 A;  1E2J A;  1E2N A;  1KI6 A;  3M4J A;  1OSN A;  1R4M B;  2XTJ A;  3L04 A;  1KI4 A;  1QHI A;  1P6X A;  1P73 A;  3FSG A;  2VTK A;  1KI2 A;  3KZC A;  1E2H A;  4IVP A;  1YVE I;  1E2I A;  3VTK A;  3FR8 A;  2G7M C;  2FG6 C;  1DBI A;  1E2P A;  1P75 A;  1F48 A;  3L06 A;  3KZK A;  3RDP A; 
#chains in the KnotProt database with same CATH homology
 4IVR A;  1OF1 A;  1KI7 A;  2KI5 A;  1E2K A;  1E2L A;  3F0T A;  4JBY A;  4IVQ A;  1E2M A;  1KIM A;  1KI6 B;  1II9 A;  1VTK A;  1GKU B;  1P72 A;  4JBX A;  1KI3 A;  1P7C A;  1KI8 A;  1E2J A;  1E2N A;  1KI6 A;  1OSN A;  1KI4 A;  1QHI A;  1P6X A;  1P73 A;  4IVP A;  2VTK A;  1KI2 A;  1E2H A;  1E2I A;  3VTK A;  1E2P A;  1P75 A;  1F48 A;  3RDP 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)

 
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#similar chains, but unknotted
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