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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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
3RDPA 1P7CA 4IVQA 1E2KA 4JBYA 1E2JA 1KI6A 1QHIA 1VTKA 1KI4A 1P6XA 1F48A 1KIMA 1E2NA 1KI6B 2KI5A 1OSNA 1OF1A 1E2MA 1II9A 1P75A 1KI2A 1E2LA 1KI7A 4JBXA 1KI8A 3VTKA 4IVRA 3F0TA 1E2PA 4IVPA 1E2HA 1KI3A 1GKUB 1P73A 1P72A 1E2IA 2VTKA
chains in the KnotProt database with same CATH superfamily
3M4JA 1YRLA 3L05A 3KZNA 3RDPA 2G7MC 1P7CA 3FR8A 4IVQA 1E2KA 4JBYA 1E2JA 1KI6A 1QHIA 1VTKA 1KI4A 1P6XA 3M5CA 3KZMA 1F48A 2FG6C 3M4NA 3KZCA 1KIMA 1E2NA 1KI6B 1DBIA 1R4NB 2KI5A 3L02A 1OSNA 1LNSA 1OF1A 1YVEI 3L06A 1E2MA 1YH1A 1JS1X 3FSGA 1II9A 1P75A 1KI2A 1R4MB 1E2LA 1KI7A 4JBXA 3FR7A 1KI8A 3VTKA 4IVRA 3F0TA 3KZKA 3KZOA 1E2PA 3M5DA 1E2HA 1KI3A 4IVPA 2XTJA 1GKUB 1QMGA 1P73A 1P72A 1E2IA 2VTKA 3L04A
chains in the KnotProt database with same CATH topology
3RDPA 1P7CA 4IVQA 1E2KA 4JBYA 1E2JA 1KI6A 1QHIA 1VTKA 1KI4A 1P6XA 1F48A 1KIMA 1E2NA 1KI6B 2KI5A 1OSNA 1OF1A 1E2MA 1II9A 1P75A 1KI2A 1E2LA 1KI7A 4JBXA 1KI8A 3VTKA 4IVRA 3F0TA 1E2PA 4IVPA 1E2HA 1KI3A 1GKUB 1P73A 1P72A 1E2IA 2VTKA
chains in the KnotProt database with same CATH homology

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