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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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

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