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(-) Description

Title :  CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH F-SK78
 
Authors :  L. Pernot, I. Novakovic, Y. Westermaier, R. Perozzo, S. Raic-Malic, L.
Date :  20 Feb 13  (Deposition) - 06 Mar 13  (Release) - 02 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Synthesis, Pet Imaging Tracer, Atp Binding, Nucleotide Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Pernot, I. Novakovic, R. Perozzo, S. Raic-Malic, L. Scapozza
New Thymine Derivatives As Hsv1-Tk Ligand For The Development Of Pet Imaging Tracer
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THYMIDINE KINASE
    Chains: A, B
    EC Number: 2.7.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-2
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 45-376
    Gene: TK, TK (UL23), UL23
    Organism Common: HHV-1
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10299
    Strain: 17
    Synonym: HSV1-TK

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2FSK2Ligand/Ion6-[(1Z)-3-FLUORO-2-(HYDROXYMETHYL)PROP-1-EN-1-YL]-1,5-DIMETHYLPYRIMIDINE-2,4(1H,3H)-DIONE
3SO45Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:58 , TRP A:88 , ILE A:97 , GLN A:125 , MET A:128 , ARG A:163 , ALA A:168 , TYR A:172 , ARG A:222 , HOH A:706 , HOH A:735 , HOH A:764BINDING SITE FOR RESIDUE FSK A 601
2AC2SOFTWAREHIS A:58 , GLY A:59 , GLY A:61 , ARG A:220 , ARG A:222 , HOH A:705 , HOH A:854 , HOH A:861BINDING SITE FOR RESIDUE SO4 A 602
3AC3SOFTWAREHIS A:105 , ARG A:226 , SER B:74 , ARG B:75BINDING SITE FOR RESIDUE SO4 A 603
4AC4SOFTWAREHIS B:58 , GLU B:83 , TRP B:88 , ILE B:97 , GLN B:125 , MET B:128 , TYR B:132 , ARG B:163 , ALA B:168 , TYR B:172 , ARG B:222 , HOH B:519 , HOH B:565 , HOH B:640BINDING SITE FOR RESIDUE FSK B 401
5AC5SOFTWARELYS A:219 , HIS B:58 , GLY B:59 , GLY B:61 , LYS B:62 , THR B:63 , ARG B:222 , HOH B:544 , HOH B:559 , HOH B:640BINDING SITE FOR RESIDUE SO4 B 402
6AC6SOFTWARELYS B:317 , ARG B:320 , SER B:321 , HOH B:511 , HOH B:617BINDING SITE FOR RESIDUE SO4 B 403
7AC7SOFTWAREHOH A:850 , ARG B:216 , ARG B:220 , HOH B:649BINDING SITE FOR RESIDUE SO4 B 404
8AC8SOFTWAREHIS B:105 , ARG B:106 , ARG B:226BINDING SITE FOR RESIDUE EDO B 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JBY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JBY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JBY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JBY)

(-) Exons   (0, 0)

(no "Exon" information available for 4JBY)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4jbya_ A: Thymidine kinase                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.......hhhhhhhhhhhh....eeee..hhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhh........eeeeee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhh....eee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jby A  45 KMPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
                                    54        64        74        84        94       104       114       124       134       144  ||   159       169       179       189       199       209       219       229       239       249       259    || 284       294       304       314       324       334       344       354       364       374
                                                                                                                                147|                                                                                                            264|                                                                                              
                                                                                                                                 153                                                                                                             280                                                                                              


Chain B from PDB  Type:PROTEIN  Length:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4jbyb_ B: Thymidine kinase                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhh......eeee..hhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeeee..hhhhhhhhhhhhhhh...hhhhhhhhhhh........eeeeee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jby B  46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
                                    55        65        75        85        95       105       115       125       135       145 ||    160       170       180       190       200       210       220       230       240       250       260   ||  279       289       299       309       319       329       339       349       359       369     
                                                                                                                               147|                                                                                                            264|                                                                                                    
                                                                                                                                153                                                                                                             274
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JBY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JBY)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  KITH_HHV11 | P03176
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KITH_HHV11 | P03176: 1e2h 1e2i 1e2j 1e2k 1e2l 1e2m 1e2n 1e2p 1ki2 1ki3 1ki4 1ki6 1ki7 1ki8 1kim 1of1 1p7c 1qhi 1vtk 2ki5 2vtk 3f0t 3rdp 3vtk 4ivp 4ivq 4ivr 4jbx 4oql 4oqm 4oqn 4oqx

(-) Related Entries Specified in the PDB File

1e2p CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH DHBT
3f0t CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH N-METHYL-DHBT
3rdp CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH N-METHYL-FHBT
4ivp CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH IN51/20
4ivq CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH IN43/5
4ivr CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH IN52/10
4jbx CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH SK78