1E2HA

The nucleoside binding site of herpes simplex type 1 thymidine kinase analyzed by x-ray crystallography
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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 5-116 112 1-4 305-329 117-304 4 25 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKTTTTQLL-----RDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSPPPAL---TLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGPRPHIGDT---------------LFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
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 7-111 105 1-6 146-306 112-145 6 161 slipknot
view details
3.1 8-146 139 1-7 183-306 147-182 7 124 slipknot
view details
3.1 4-182 179 1-3 223-306 183-222 3 84 slipknot
view details
2.1 9-183 175 1-8 252-306 184-251 8 55 slipknot
view details
2.1 8-252 245 1-7 282-306 253-281 7 25 slipknot
sequence length 329
structure length 306
publication title Nucleoside Binding Site of Herpes Simplex Type 1 Thymidine Kinase Analyzed by X-Ray Crystallography
pubmed doi rcsb
molecule tags Transferase
molecule keywords THYMIDINE KINASE
source organism Herpes simplex virus (type 1 / strain 17)
missing residues 25-29, 105-107, 220-234
total genus Genus: 113
ec nomenclature ec 2.7.1.21: Thymidine kinase.
pdb deposition date 2000-05-23
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 1e2hA00
2VTKA 1QHIA 1KI7A 1E2LA 1VTKA 1P7CA 3F0TA 1E2IA 4IVQA 1KI2A 1GKUB 4JBXA 4JBYA 1KIMA 1KI6A 1E2PA 1E2JA 1KI8A 1P6XA 1P73A 1E2NA 1E2MA 3RDPA 1P72A 1E2HA 1II9A 1KI3A 2KI5A 1KI4A 1KI6B 4IVPA 1OF1A 1F48A 3VTKA 1P75A 4IVRA 1E2KA 1OSNA
chains in the KnotProt database with same CATH superfamily
3L06A 3M5DA 2VTKA 3KZNA 1QHIA 1YVEI 1KI7A 1E2LA 1VTKA 2G7MC 1YRLA 1P7CA 3L02A 3F0TA 1E2IA 3M4JA 4IVQA 1KI2A 1GKUB 4JBXA 4JBYA 1KIMA 1KI6A 3KZKA 1E2PA 1E2JA 3M4NA 3KZMA 3FR8A 1QMGA 2FG6C 3FSGA 3FR7A 1YH1A 1KI8A 1P6XA 1P73A 1R4MB 1E2NA 1E2MA 3RDPA 1P72A 2XTJA 3L05A 1E2HA 1II9A 1R4NB 1JS1X 1KI3A 2KI5A 3KZCA 1KI4A 3M5CA 4IVPA 1OF1A 1F48A 1LNSA 1P75A 3VTKA 4IVRA 3KZOA 1KI6B 1E2KA 1OSNA 1DBIA 3L04A
chains in the KnotProt database with same CATH topology
2VTKA 1QHIA 1KI7A 1E2LA 1VTKA 1P7CA 3F0TA 1E2IA 4IVQA 1KI2A 1GKUB 4JBXA 4JBYA 1KIMA 1KI6A 1E2PA 1E2JA 1KI8A 1P6XA 1P73A 1E2NA 1E2MA 3RDPA 1P72A 1E2HA 1II9A 1KI3A 2KI5A 1KI4A 1KI6B 4IVPA 1OF1A 1F48A 3VTKA 1P75A 4IVRA 1E2KA 1OSNA
chains in the KnotProt database with same CATH homology


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

 
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