1KI6A

Crystal structure of thymidine kinase from herpes simplex virus type i complexed with a 5-iodouracil anhydrohexitol nucleoside
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 5-117 113 1-4 305-329 118-304 4 25 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKTTTTQLL-------DIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAPPALTLI------FDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSARPHIGDTLFTLF----------------RAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
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 7-105 99 1-6 175-300 106-174 6 126 slipknot
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3.1 5-174 170 1-4 194-300 175-193 4 107 slipknot
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2.1 8-175 168 1-7 276-300 176-275 7 25 slipknot
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2.1 9-201 193 1-7, 266-300 8-8, 202-265 7 35 slipknot
sequence length 329
structure length 300
publication title Exploring the active site of herpes simplex virus type-1 thymidine kinase by X-ray crystallography of complexes with aciclovir and other ligands.
pubmed doi rcsb
molecule tags Phosphotransferase
molecule keywords THYMIDINE KINASE
source organism Herpes simplex virus (type 1 / strain 17)
missing residues 25-31, 103-108, 219-234
total genus Genus: 108
ec nomenclature ec 2.7.1.21: Thymidine kinase.
pdb deposition date 1998-05-18
KnotProt deposition date 2014-07-31

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 1ki6A00
3RDPA 1E2HA 1VTKA 1KI8A 1E2JA 1P7CA 1KIMA 3F0TA 1E2PA 1KI6A 4IVRA 1KI3A 1P72A 1E2NA 1P73A 1E2IA 1GKUB 4JBXA 1KI6B 1E2LA 1E2MA 1KI7A 2VTKA 1P75A 2KI5A 4JBYA 4IVQA 1E2KA 1OF1A 1II9A 1KI4A 1KI2A 1P6XA 4IVPA 1QHIA 1OSNA 3VTKA 1F48A
chains in the KnotProt database with same CATH superfamily
3RDPA 3L04A 1E2HA 1VTKA 1YRLA 3L02A 3M5CA 1KI8A 2XTJA 1E2JA 2G7MC 1P7CA 1KIMA 1YVEI 3F0TA 1E2PA 1KI6A 4IVRA 1KI3A 1P72A 3KZNA 3M5DA 1E2NA 1P73A 1R4MB 1JS1X 3FR7A 3KZMA 1E2IA 1GKUB 3KZOA 4JBXA 1KI6B 1E2LA 1E2MA 1KI7A 2VTKA 1P75A 3L06A 2KI5A 1YH1A 3FR8A 3M4NA 4JBYA 4IVQA 1E2KA 1OF1A 3M4JA 1II9A 1KI4A 1KI2A 1P6XA 1R4NB 1QMGA 4IVPA 3L05A 1QHIA 2FG6C 3KZCA 3KZKA 1OSNA 1DBIA 1LNSA 3FSGA 3VTKA 1F48A
chains in the KnotProt database with same CATH topology
3RDPA 1E2HA 1VTKA 1KI8A 1E2JA 1P7CA 1KIMA 3F0TA 1E2PA 1KI6A 4IVRA 1KI3A 1P72A 1E2NA 1P73A 1E2IA 1GKUB 4JBXA 1KI6B 1E2LA 1E2MA 1KI7A 2VTKA 1P75A 2KI5A 4JBYA 4IVQA 1E2KA 1OF1A 1II9A 1KI4A 1KI2A 1P6XA 4IVPA 1QHIA 1OSNA 3VTKA 1F48A
chains in the KnotProt database with same CATH homology

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