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(-) Description

Title :  CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH ME-ARA-EDU
 
Authors :  L. Pernot, A. B. Neef, Y. Westermaier, R. Perozzo, N. Luedtke, L. Scapoz
Date :  10 Feb 14  (Deposition) - 13 Aug 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
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 :  A. B. Neef, L. Pernot, L. Scapozza, N. W. Luedkte
Crystal Structure Of Hsv1-Tk Complexed With Me-Ara-Edu
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

 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
1EDV2Ligand/Ion1-(2-DEOXY-2-METHYL-BETA-D-ARABINOFURANOSYL)-5-ETHYNYLPYRIMIDINE-2,4(1H,3H)-DIONE
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:222BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREHIS A:105 , ARG A:226 , SER B:74 , ARG B:75BINDING SITE FOR RESIDUE SO4 A 402
3AC3SOFTWAREARG A:212 , ARG A:216 , ARG B:220BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWAREHIS A:58 , ILE A:97 , ILE A:100 , TYR A:101 , GLN A:125 , MET A:128 , ARG A:163 , ALA A:167 , ALA A:168 , TYR A:172 , ARG A:222 , GLU A:225 , HOH A:511BINDING SITE FOR RESIDUE EDV A 404
5AC5SOFTWAREHIS B:58 , GLY B:59 , MET B:60 , GLY B:61 , LYS B:62 , THR B:63BINDING SITE FOR RESIDUE SO4 B 401
6AC6SOFTWARELYS B:317 , ARG B:320 , HOH B:538BINDING SITE FOR RESIDUE SO4 B 402
7AC7SOFTWAREHIS B:58 , ILE B:97 , TYR B:101 , GLN B:125 , MET B:128 , TYR B:132 , ARG B:163 , ALA B:168 , TYR B:172 , GLU B:225 , HOH B:503BINDING SITE FOR RESIDUE EDV B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OQX)

(-) 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:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhh.....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
                 4oqx A  45 KMPTLLRVYIDGPHGMGKTTTTQLLVASRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
                                    54        64      ||76        86        96       106       116       126       136       146||     161       171       181       191       201       211       221       231       241       251       261  ||   286       296       306       316       326       336       346       356       366        
                                                     71|                                                                      147|                                                                                                            264|                                                                                              
                                                      74                                                                       153                                                                                                             280                                                                                              


Chain B from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhh......eeee..hhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhh........eeeeee.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh....eee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oqx B  46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
                                    55        65        75        85        95       105       115       125       135       145 ||    160       170       180       190       200       210       220|      233       243       253       263||     286       296       306       316       326       336       346       356       366        
                                                                                                                               147|                                                                220|                                     264|                                                                                                
                                                                                                                                153                                                                 224                                      278
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4jby 4oql 4oqm 4oqn

(-) Related Entries Specified in the PDB File

4oql 4oqm 4oqn