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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.
Genus: 107
Slipknot S +31

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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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+31 5-117 113 1-4 306-329 118-305 4 24 slipknot
Chain Sequence
MPTLLRVYIDGPHGMGKT------------DDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGPPPALTLIFDRH----PIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTGPRPHIGDTLFTLFRA-------------PELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE
Whole chain analysis

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Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1


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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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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
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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
1P72A 3VTKA 1OSNA 3RDPA 4JBYA 1F48A 1E2LA 1VTKA 2VTKA 1P7CA 4IVQA 1KI6A 1KI8A 1E2IA 1P73A 1II9A 1KIMA 1P6XA 1E2KA 1E2JA 1KI2A 1KI7A 1E2MA 1E2NA 2KI5A 4IVRA 1KI3A 3F0TA 1KI4A 1E2PA 1OF1A 1QHIA 1E2HA 1KI6B 1GKUB 1P75A 4IVPA 4JBXA
chains in the KnotProt database with same CATH superfamily
1P72A 3L05A 3VTKA 1YRLA 1OSNA 3RDPA 3M5DA 3FR7A 4JBYA 3KZKA 1F48A 1E2LA 1VTKA 3L04A 1QMGA 2VTKA 1P7CA 4IVQA 1DBIA 1KI6A 1KI8A 1E2IA 3L06A 1P73A 1YH1A 3L02A 1II9A 2G7MC 1YVEI 1KIMA 1P6XA 1E2KA 1E2JA 1KI2A 3FSGA 1JS1X 1KI7A 3M4NA 1E2MA 1E2NA 2KI5A 3FR8A 2FG6C 4IVRA 1KI3A 3KZNA 1R4MB 3F0TA 1KI4A 3KZCA 3M4JA 1E2PA 3KZMA 3KZOA 1OF1A 1QHIA 1R4NB 1E2HA 1KI6B 1GKUB 1P75A 2XTJA 1LNSA 4IVPA 4JBXA 3M5CA
chains in the KnotProt database with same CATH topology
1P72A 3VTKA 1OSNA 3RDPA 4JBYA 1F48A 1E2LA 1VTKA 2VTKA 1P7CA 4IVQA 1KI6A 1KI8A 1E2IA 1P73A 1II9A 1KIMA 1P6XA 1E2KA 1E2JA 1KI2A 1KI7A 1E2MA 1E2NA 2KI5A 4IVRA 1KI3A 3F0TA 1KI4A 1E2PA 1OF1A 1QHIA 1E2HA 1KI6B 1GKUB 1P75A 4IVPA 4JBXA
chains in the KnotProt database with same CATH homology

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