1E2IA

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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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 5-117 113 1-4 306-329 118-305 4 24 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKT------------DDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGPPPALTLIFDRH----PIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTGPRPHIGDTLFTLFRA-------------PELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
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 7-103 97 1-6 139-300 104-138 6 162 slipknot
view details
3.1 4-140 137 1-3 161-300 141-160 3 140 slipknot
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2.1 8-142 135 1-7 250-300 143-249 7 51 slipknot
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3.1 4-249 246 1-3 275-300 250-274 3 26 slipknot
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2.1 8-250 243 1-7 276-300 251-275 7 25 slipknot
view details
2.1 5-139 135 1-2, 142-300 3-4, 140-141 2 159 slipknot
view details
2.1 9-253 245 1-7, 266-300 8-8, 254-265 7 35 slipknot
sequence length 329
structure length 300
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 19-30, 104-107, 221-233
total genus Genus: 107
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 1e2iA00
1E2PA 1P73A 1E2IA 4JBYA 3RDPA 1OSNA 1P72A 1F48A 4JBXA 1P7CA 1GKUB 1E2HA 1VTKA 4IVPA 1KI2A 1II9A 1KI6B 3VTKA 1E2JA 1E2MA 1KI8A 4IVRA 1KI7A 2KI5A 1KIMA 1E2LA 1KI3A 1E2NA 3F0TA 1KI6A 2VTKA 1OF1A 1QHIA 1KI4A 1E2KA 1P6XA 1P75A 4IVQA
chains in the KnotProt database with same CATH superfamily
1E2PA 1P73A 1E2IA 4JBYA 3RDPA 3KZMA 1R4MB 1OSNA 1P72A 3FSGA 3M5CA 1F48A 4JBXA 1LNSA 3M4JA 3KZNA 1P7CA 3KZKA 1GKUB 3L02A 3M4NA 2G7MC 1E2HA 1VTKA 4IVPA 1KI2A 3KZCA 1II9A 1R4NB 1YH1A 2FG6C 3VTKA 1E2JA 1KI6B 3FR7A 1E2MA 1KI8A 4IVRA 3FR8A 1KI7A 2KI5A 3L06A 3KZOA 1JS1X 1KIMA 3L05A 1E2LA 1KI3A 1E2NA 3F0TA 1DBIA 1QMGA 1KI6A 2VTKA 3M5DA 1YRLA 1OF1A 1QHIA 1YVEI 1KI4A 1E2KA 1P6XA 2XTJA 1P75A 4IVQA 3L04A
chains in the KnotProt database with same CATH topology
1E2PA 1P73A 1E2IA 4JBYA 3RDPA 1OSNA 1P72A 1F48A 4JBXA 1P7CA 1GKUB 1E2HA 1VTKA 4IVPA 1KI2A 1II9A 1KI6B 3VTKA 1E2JA 1E2MA 1KI8A 4IVRA 1KI7A 2KI5A 1KIMA 1E2LA 1KI3A 1E2NA 3F0TA 1KI6A 2VTKA 1OF1A 1QHIA 1KI4A 1E2KA 1P6XA 1P75A 4IVQA
chains in the KnotProt database with same CATH homology


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