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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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

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