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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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
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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
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
2VTKA 3VTKA 1II9A 1F48A 4IVPA 1KI7A 1E2PA 1P75A 1KI4A 1KI6A 1E2HA 1P6XA 4IVRA 1E2MA 4JBYA 1VTKA 1OF1A 1P73A 1E2NA 1KIMA 3RDPA 1E2KA 1GKUB 1OSNA 1KI2A 1E2JA 1E2LA 1KI8A 1P7CA 1KI3A 4IVQA 2KI5A 1P72A 3F0TA 1KI6B 1QHIA 4JBXA 1E2IA
chains in the KnotProt database with same CATH superfamily
2VTKA 3KZCA 3M5DA 1DBIA 3VTKA 1II9A 1JS1X 1F48A 3L04A 4IVPA 1KI7A 1E2PA 1YVEI 1P75A 2FG7C 1KI4A 1KI6A 1E2HA 3FSGA 3L06A 3M4NA 1P6XA 4IVRA 1YH1A 3KZMA 2FG6C 1E2MA 4JBYA 1VTKA 3KZKA 3KZOA 1QMGA 1OF1A 1P73A 1E2NA 3L02A 2FG7X 3M4JA 3FR8A 3FR7A 1KIMA 1YRLA 2XTJA 3L05A 2G7MC 1E2KA 3RDPA 1GKUB 1OSNA 3KZNA 1KI2A 1E2JA 1E2LA 1KI8A 1P7CA 1R4NB 1KI3A 4IVQA 1LNSA 2KI5A 1P72A 1R4MB 3F0TA 1KI6B 3M5CA 1QHIA 4JBXA 1E2IA
chains in the KnotProt database with same CATH topology
2VTKA 3VTKA 1II9A 1F48A 4IVPA 1KI7A 1E2PA 1P75A 1KI4A 1KI6A 1E2HA 1P6XA 4IVRA 1E2MA 4JBYA 1VTKA 1OF1A 1P73A 1E2NA 1KIMA 3RDPA 1E2KA 1GKUB 1OSNA 1KI2A 1E2JA 1E2LA 1KI8A 1P7CA 1KI3A 4IVQA 2KI5A 1P72A 3F0TA 1KI6B 1QHIA 4JBXA 1E2IA
chains in the KnotProt database with same CATH homology


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