4IVRA

Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with in52/10
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 1-3 305-329 118-304 3 25 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEA-----PPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKPGERL---DLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGNAGPRPHI------------GDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
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
3.1 7-113 107 1-6 143-309 114-142 6 167 slipknot
view details
3.1 4-142 139 1-3 148-309 143-147 3 162 slipknot
view details
2.1 9-152 144 1-8 271-309 153-270 8 39 slipknot
view details
3.1 4-270 267 1-3 283-309 271-282 3 27 slipknot
view details
3.1 6-278 273 1-5 285-309 279-284 5 25 slipknot
view details
3.1 7-271 265 1-3, 278-309 4-6, 272-277 3 32 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, 175-177, 220-231
total genus Genus: 108
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 4ivrA00
1VTKA 4JBXA 4IVRA 1II9A 4IVQA 1P72A 1P75A 4JBYA 1E2HA 1KI2A 1OSNA 1F48A 2VTKA 1KI6A 1QHIA 1P7CA 1KI7A 1E2PA 1P6XA 2KI5A 1E2KA 3VTKA 3F0TA 4IVPA 1E2LA 1E2NA 1E2JA 3RDPA 1KI4A 1KIMA 1KI6B 1GKUB 1P73A 1E2IA 1KI3A 1OF1A 1KI8A 1E2MA
chains in the KnotProt database with same CATH superfamily
1VTKA 3KZCA 4JBXA 4IVRA 1II9A 3M4NA 4IVQA 3L05A 1QMGA 3FSGA 1P72A 1P75A 3M4JA 3M5DA 3M5CA 3L04A 2FG7C 1YVEI 4JBYA 1DBIA 1YRLA 1JS1X 1E2HA 1KI2A 1OSNA 2FG7X 3L02A 3KZNA 3L06A 1F48A 2VTKA 1KI6A 3FR8A 1QHIA 1P7CA 1KI7A 1E2PA 2XTJA 1P6XA 2KI5A 3KZMA 1LNSA 1R4MB 1E2KA 3VTKA 1R4NB 3FR7A 3F0TA 4IVPA 1E2LA 1E2NA 1E2JA 3RDPA 1KI4A 1KIMA 2FG6C 1KI6B 1GKUB 1P73A 1E2IA 1YH1A 1KI3A 1OF1A 2G7MC 3KZKA 3KZOA 1KI8A 1E2MA
chains in the KnotProt database with same CATH topology
1VTKA 4JBXA 4IVRA 1II9A 4IVQA 1P72A 1P75A 4JBYA 1E2HA 1KI2A 1OSNA 1F48A 2VTKA 1KI6A 1QHIA 1P7CA 1KI7A 1E2PA 1P6XA 2KI5A 1E2KA 3VTKA 3F0TA 4IVPA 1E2LA 1E2NA 1E2JA 3RDPA 1KI4A 1KIMA 1KI6B 1GKUB 1P73A 1E2IA 1KI3A 1OF1A 1KI8A 1E2MA
chains in the KnotProt database with same CATH homology


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