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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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
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2.1 9-253 245 1-7, 266-300 8-8, 254-265 7 35 slipknot
missing residues 19-30, 104-107, 221-233
publication title Nucleoside Binding Site of Herpes Simplex Type 1 Thymidine Kinase Analyzed by X-Ray Crystallography
pubmed doi rcsb
structure length 300
molecule tags Transferase
source organism Herpes simplex virus (type 1 / strain 17)
sequence length 329
molecule keywords THYMIDINE KINASE
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
3RDPA 1E2NA 1KI6A 4IVPA 1VTKA 1GKUB 1II9A 1KI6B 3F0TA 1E2HA 1KI4A 1QHIA 1OF1A 4JBXA 1E2IA 1KI3A 1P75A 2VTKA 1F48A 1E2LA 1KI8A 4IVRA 1E2PA 4JBYA 1E2JA 1KI2A 1P72A 1E2KA 1P7CA 2KI5A 1E2MA 1KI7A 4IVQA 1KIMA 1P6XA 1OSNA 1P73A 3VTKA
chains in the KnotProt database with same CATH superfamily
3RDPA 3M4NA 3FSGA 3L04A 1E2NA 1KI6A 4IVPA 3KZKA 1QMGA 3KZCA 1DBIA 1R4MB 3L02A 2FG7C 1VTKA 1GKUB 4JBXA 3FR8A 1II9A 2FG6C 2G7MC 1KI6B 3F0TA 1LNSA 1E2HA 1KI4A 1JS1X 3KZMA 3M5DA 3FR7A 1QHIA 1YRLA 1OF1A 3M5CA 3L05A 4IVRA 1E2IA 1KI3A 1P75A 2VTKA 1YH1A 1F48A 1YVEI 1E2LA 1KI8A 3M4JA 2XTJA 1E2PA 4JBYA 2FG7X 1E2JA 1KI2A 1P72A 1E2KA 3KZOA 1P7CA 2KI5A 3L06A 1E2MA 1KI7A 4IVQA 1R4NB 1KIMA 1P6XA 3VTKA 1OSNA 1P73A 3KZNA
chains in the KnotProt database with same CATH topology
3RDPA 1E2NA 1KI6A 4IVPA 1VTKA 1GKUB 1II9A 1KI6B 3F0TA 1E2HA 1KI4A 1QHIA 1OF1A 4JBXA 1E2IA 1KI3A 1P75A 2VTKA 1F48A 1E2LA 1KI8A 4IVRA 1E2PA 4JBYA 1E2JA 1KI2A 1P72A 1E2KA 1P7CA 2KI5A 1E2MA 1KI7A 4IVQA 1KIMA 1P6XA 1OSNA 1P73A 3VTKA
chains in the KnotProt database with same CATH homology


 
#chains in the KnotProt database with same CATH superfamily
 3RDP A;  1E2N A;  1KI6 A;  4IVP A;  1VTK A;  1GKU B;  1II9 A;  1KI6 B;  3F0T A;  1E2H A;  1KI4 A;  1QHI A;  1OF1 A;  4JBX A;  1E2I A;  1KI3 A;  1P75 A;  2VTK A;  1F48 A;  1E2L A;  1KI8 A;  4IVR A;  1E2P A;  4JBY A;  1E2J A;  1KI2 A;  1P72 A;  1E2K A;  1P7C A;  2KI5 A;  1E2M A;  1KI7 A;  4IVQ A;  1KIM A;  1P6X A;  1OSN A;  1P73 A;  3VTK A; 
#chains in the KnotProt database with same CATH topology
 3RDP A;  3M4N A;  3FSG A;  3L04 A;  1E2N A;  1KI6 A;  4IVP A;  3KZK A;  1QMG A;  3KZC A;  1DBI A;  1R4M B;  3L02 A;  2FG7 C;  1VTK A;  1GKU B;  4JBX A;  3FR8 A;  1II9 A;  2FG6 C;  2G7M C;  1KI6 B;  3F0T A;  1LNS A;  1E2H A;  1KI4 A;  1JS1 X;  3KZM A;  3M5D A;  3FR7 A;  1QHI A;  1YRL A;  1OF1 A;  3M5C A;  3L05 A;  4IVR A;  1E2I A;  1KI3 A;  1P75 A;  2VTK A;  1YH1 A;  1F48 A;  1YVE I;  1E2L A;  1KI8 A;  3M4J A;  2XTJ A;  1E2P A;  4JBY A;  2FG7 X;  1E2J A;  1KI2 A;  1P72 A;  1E2K A;  3KZO A;  1P7C A;  2KI5 A;  3L06 A;  1E2M A;  1KI7 A;  4IVQ A;  1R4N B;  1KIM A;  1P6X A;  3VTK A;  1OSN A;  1P73 A;  3KZN A; 
#chains in the KnotProt database with same CATH homology
 3RDP A;  1E2N A;  1KI6 A;  4IVP A;  1VTK A;  1GKU B;  1II9 A;  1KI6 B;  3F0T A;  1E2H A;  1KI4 A;  1QHI A;  1OF1 A;  4JBX A;  1E2I A;  1KI3 A;  1P75 A;  2VTK A;  1F48 A;  1E2L A;  1KI8 A;  4IVR A;  1E2P A;  4JBY A;  1E2J A;  1KI2 A;  1P72 A;  1E2K A;  1P7C A;  2KI5 A;  1E2M A;  1KI7 A;  4IVQ A;  1KIM A;  1P6X A;  1OSN A;  1P73 A;  3VTK 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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