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(-) Description

Title :  CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH EDU
 
Authors :  L. Pernot, A. B. Neef, Y. Westermaier, R. Perozzo, N. W. Luedtke, L. Scap
Date :  10 Feb 14  (Deposition) - 13 Aug 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Synthesis, Thymidine Kinase, Atp-Binding, Nucleotide-Binding, Transferase, 5-Ethynyluridine Nucleoside Derivative (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Pernot, A. B. Neef, Y. Westermaier, R. Perozzo, N. W. Luedtke, L. Scapozza
Crystal Structure Of Thymidine Kinase From Herpes Simplex Virus Type 1 In Complex With Edu
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THYMIDINE KINASE
    ChainsA, B
    EC Number2.7.1.21
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-2
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 45-376
    GeneTK, TK (UL23), UL23
    Organism CommonHHV-1
    Organism ScientificHUMAN HERPESVIRUS 1
    Organism Taxid10299
    Strain17

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1EDU2Ligand/Ion2'-DEOXY-5-ETHYNYLURIDINE
2SO45Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:58 , GLY A:59 , MET A:60 , GLY A:61 , LYS A:62 , THR A:63 , ARG A:220 , ARG A:222 , HOH A:539BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREHIS A:105 , ARG A:226 , ARG B:75BINDING SITE FOR RESIDUE SO4 A 402
3AC3SOFTWAREARG A:212 , ARG A:216 , ARG B:220 , GLN B:221BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWAREHIS A:58 , GLU A:83 , ILE A:97 , ILE A:100 , TYR A:101 , GLN A:125 , MET A:128 , ARG A:163 , ALA A:168 , TYR A:172 , GLU A:225 , HOH A:504 , HOH A:519 , HOH A:539BINDING SITE FOR RESIDUE EDU A 404
5AC5SOFTWAREHIS B:58 , GLY B:59 , MET B:60 , GLY B:61 , LYS B:62 , THR B:63 , HOH B:561BINDING SITE FOR RESIDUE SO4 B 401
6AC6SOFTWARELYS B:317 , ARG B:320 , SER B:321 , HOH B:507 , HOH B:547BINDING SITE FOR RESIDUE SO4 B 402
7AC7SOFTWAREHIS B:58 , GLU B:83 , ILE B:97 , ILE B:100 , TYR B:101 , GLN B:125 , MET B:128 , ARG B:163 , ALA B:168 , TYR B:172 , GLU B:225 , HOH B:504 , HOH B:513 , HOH B:561BINDING SITE FOR RESIDUE EDU B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OQN)

(-) 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhh....eeee..hhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeeee..hhhhhhhhhhhhhhh...hhhhhhhhhhh........eeeeee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oqn 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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhhhh....eeee..hhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeeee..hhhhhhhhhhhhhhh...hhhhhhhhhhh........eeeeee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oqn 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)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (0, 0)

(no "SCOP Domain" information available for 4OQN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        KITH_HHV11 | P031761e2h 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 4jby 4oql 4oqm 4oqx

(-) Related Entries Specified in the PDB File

4oql 4oqm 4oqx