1E2JA

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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 1-4 306-329 117-305 4 24 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKTTTTQLL-----RDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSANITMGMPYAVTDAVLAPHIGGEAGSPPPAL---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
2.1 7-111 105 1-6 147-306 112-146 6 160 slipknot
view details
3.1 7-153 147 1-6 177-306 154-176 6 130 slipknot
view details
2.1 8-176 169 1-7 250-306 177-249 7 57 slipknot
view details
3.1 6-250 245 1-5 280-306 251-279 5 27 slipknot
view details
2.1 8-157 150 1-6, 175-306 7-7, 158-174 6 132 slipknot
view details
2.1 9-201 193 1-7, 250-306 8-8, 202-249 7 57 slipknot
view details
2.1 8-251 244 1-5, 279-306 6-7, 252-278 5 28 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: 111
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 1e2jA00
1P75A 1F48A 2VTKA 1KI3A 1II9A 1OF1A 1KI2A 1KI6A 1KIMA 1E2LA 1E2JA 4IVRA 1E2NA 1P72A 1P7CA 1KI6B 1GKUB 3RDPA 1KI4A 4JBXA 1OSNA 1E2HA 1P73A 1VTKA 1KI7A 1P6XA 3VTKA 1E2PA 1E2IA 4IVPA 1QHIA 1E2MA 3F0TA 4JBYA 2KI5A 1E2KA 4IVQA 1KI8A
chains in the KnotProt database with same CATH superfamily
1P75A 3KZOA 1F48A 2VTKA 1KI3A 1II9A 3KZCA 3L04A 3M4NA 1OF1A 1KI2A 1KI6A 3M5DA 2XTJA 1KIMA 1E2LA 1E2JA 4IVRA 3FR8A 1E2NA 1P72A 1P7CA 3L02A 1KI6B 1GKUB 1YH1A 2FG6C 3RDPA 1JS1X 3KZKA 1R4MB 1KI4A 3FR7A 4JBXA 1E2HA 1OSNA 1P73A 3FSGA 1VTKA 3M5CA 3M4JA 1KI7A 1P6XA 3KZMA 1YVEI 3VTKA 1DBIA 1E2PA 3L06A 1QMGA 1E2IA 4IVPA 1QHIA 2G7MC 1R4NB 1E2MA 3KZNA 1YRLA 3F0TA 4JBYA 2KI5A 1E2KA 4IVQA 1LNSA 1KI8A 3L05A
chains in the KnotProt database with same CATH topology
1P75A 1F48A 2VTKA 1KI3A 1II9A 1OF1A 1KI2A 1KI6A 1KIMA 1E2LA 1E2JA 4IVRA 1E2NA 1P72A 1P7CA 1KI6B 1GKUB 3RDPA 1KI4A 4JBXA 1OSNA 1E2HA 1P73A 1VTKA 1KI7A 1P6XA 3VTKA 1E2PA 1E2IA 4IVPA 1QHIA 1E2MA 3F0TA 4JBYA 2KI5A 1E2KA 4IVQA 1KI8A
chains in the KnotProt database with same CATH homology


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