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(-) Description

Title :  CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH F-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 :  2.20
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. Luedtke, L. Scapozza
Crystal Structure Of Thymidine Kinase From Herpes Simplex Virus Type 1 In Complex With F-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, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1FDU2Ligand/Ion1-(2-DEOXY-2-FLUORO-BETA-D-ARABINOFURANOSYL)-5-ETHYNYLPYRIMIDINE-2,4(1H,3H)-DIONE
2SO46Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:58 , GLU A:83 , ILE A:97 , ILE A:100 , TYR A:101 , GLN A:125 , MET A:128 , TYR A:132 , ARG A:163 , ALA A:168 , TYR A:172 , ARG A:222 , GLU A:225 , HOH A:603 , HOH A:620BINDING SITE FOR RESIDUE FDU A 501
2AC2SOFTWAREHIS A:58 , GLY A:59 , MET A:60 , GLY A:61 , LYS A:62 , THR A:63 , ARG A:220 , ARG A:222BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWAREARG A:212 , ARG A:216BINDING SITE FOR RESIDUE SO4 A 503
4AC4SOFTWAREHIS A:105 , ARG A:226 , SER B:74 , ARG B:75BINDING SITE FOR RESIDUE SO4 A 504
5AC5SOFTWAREARG A:89BINDING SITE FOR RESIDUE SO4 A 505
6AC6SOFTWAREHIS B:58 , GLU B:83 , TYR B:101 , GLN B:125 , MET B:128 , ARG B:163 , ALA B:168 , TYR B:172 , GLU B:225 , HOH B:601 , HOH B:610 , HOH B:611BINDING SITE FOR RESIDUE FDU B 501
7AC7SOFTWAREHIS B:58 , GLY B:59 , MET B:60 , GLY B:61 , LYS B:62 , THR B:63 , HOH B:610 , HOH B:669BINDING SITE FOR RESIDUE SO4 B 502
8AC8SOFTWARELYS B:317 , ARG B:320 , HOH B:618BINDING SITE FOR RESIDUE SO4 B 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OQM)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhh....eeee..hhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.....eeeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhh........eeeeee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4oqm A  45 KMPTLLRVYIDGPHGMGKTTTTQLLVRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
                                    54        64     || 78        88        98       108       118       128       138       153       163       173       183       193       203       213       223       233       243       253       263||     288       298       308       318       328       338       348       358       368      
                                                    70|                                                                     147|                                                                                                            264|                                                                                              
                                                     75                                                                      153                                                                                                             280                                                                                              


Chain B from PDB  Type:PROTEIN  Length:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhhhh....eeee..hhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....eeeeee..hhhhhhhhhhhhhhh...hhhhhhhhhhh........eeeeee.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oqm B  46 MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGE 374
                                    55        65        75        85        95       105       115       125       135       145 ||    160       170       180       190       200       210       220|      232       242       252       262 ||    281       291       301       311       321       331       341       351       361       371   
                                                                                                                               147|                                                                220|                                      264|                                                                                                    
                                                                                                                                153                                                                 223                                       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 4OQM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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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 4oqn 4oqx

(-) Related Entries Specified in the PDB File

4oql 4oqn 4oqx