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(-) Description

Title :  COMPLEX STRUCTURE OF THYMIDYLATE SYNTHASE FROM VARICELLA ZOSTER VIRUS WITH A PHOSPHORYLATED BVDU
 
Authors :  K. Hew
Date :  22 Jan 15  (Deposition) - 16 Dec 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Vzv, Thymidylate Synthase, Herpesvirus, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Hew, S. L. Dahlroth, S. Veerappan, L. X. Pan, T. Cornvik, P. Nordlund
Structure Of The Varicella Zoster Virus Thymidylate Synthas Establishes Functional And Structural Similarities As The Human Enzyme And Potentiates Itself As A Target Of Brivudine.
Plos One V. 10 43947 2015
PubMed-ID: 26630264  |  Reference-DOI: 10.1371/JOURNAL.PONE.0143947

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 2.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 8-295
    Gene: ORF13
    Organism Common: HHV-3
    Organism Scientific: VARICELLA-ZOSTER VIRUS (STRAIN OKA VACCINE)
    Organism Taxid: 341980
    Strain: OKA VACCINE
    Synonym: TSASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
11PE4Ligand/IonPENTAETHYLENE GLYCOL
2BVP4Ligand/Ion(E)-5-(2-BROMOVINYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2BVP2Ligand/Ion(E)-5-(2-BROMOVINYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2BVP2Ligand/Ion(E)-5-(2-BROMOVINYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:38 , TRP A:97 , TYR A:123 , CYS A:183 , HIS A:184 , GLN A:202 , ARG A:203 , SER A:204 , GLY A:205 , ASP A:206 , GLY A:210 , ASN A:214 , HIS A:244 , TYR A:246 , HOH A:1104 , ARG B:163 , ARG B:164binding site for residue BVP A 1001
2AC2SOFTWAREILE A:96 , PHE A:213 , GLY B:12 , PHE B:13binding site for residue 1PE A 1002
3AC3SOFTWAREARG A:163 , ARG A:164 , ARG B:38 , CYS B:183 , GLN B:202 , ARG B:203 , SER B:204 , ASP B:206 , GLY B:210 , ASN B:214 , HIS B:244 , TYR B:246 , 1PE B:1002binding site for residue BVP B 1001
4AC4SOFTWARETRP B:97 , TYR B:100 , PHE B:213 , BVP B:1001binding site for residue 1PE B 1002
5AC5SOFTWAREARG C:38 , TRP C:97 , TYR C:123 , LEU C:180 , CYS C:183 , GLN C:202 , ARG C:203 , SER C:204 , GLY C:205 , ASP C:206 , GLY C:210 , ASN C:214 , HIS C:244 , TYR C:246 , 1PE C:1002 , ARG D:163 , ARG D:164binding site for residue BVP C 1001
6AC6SOFTWAREILE C:96 , LEU C:180 , PHE C:213 , BVP C:1001binding site for residue 1PE C 1002
7AC7SOFTWAREARG C:163 , ARG C:164 , ARG D:38 , CYS D:183 , GLN D:202 , ARG D:203 , SER D:204 , ASP D:206 , GLY D:210 , ASN D:214 , HIS D:244 , TYR D:246 , 1PE D:1002binding site for residue BVP D 1001
8AC8SOFTWAREILE D:96 , GLY D:210 , PHE D:213 , BVP D:1001binding site for residue 1PE D 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XSC)

(-) Sequences/Alignments

Asymmetric 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.eeee.....eeeeeeeeeeeee.............hhhhhhhhhhhhhh....hhhhhh.............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee.hhhhhhhhhh........eeee..........hhh.eeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xsc A  14 TLTGELQYLKQVDDILRYGVRKRDRTGIGTLSLFGMQARYNLRNEFPLLTTKRVFWRAVVEELLWFIRGSTDSKELAAKDIHIWDTGDLGPIYGFQWRHFGAEYKDCQSNYLQQGIDQLQTVIDTIKTNPESRRMIISSWNPKDIPLMVLPPCHTLCQFYVANGELSCQVYQRSGDMGLGVPFNIAGYALLTYIVAHVTGLKTGDLIHTMGDAHIYLNHIDALKVQLARSPKPFPCLKIIRNVTDINDFKWDDFQLDGYNPHP 293
                                    23        33        43        53        63        73        83        93    || 120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290   
                                                                                                               98|                                                                                                                                                                                 
                                                                                                               116                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.eee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeee...eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee..........hhh.eeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xsc B  12 GFTLTGELQYLKQVDDILRYGVRKRDRTGIGTLSLFGMQARYNLRNEFPLLTTKRVFWRAVVEELLWFIRGSTDSKELAAKDIHIWDIYGSSKFLNRNGFHKRHTGDLGPIYGFQWRHFGAEYKDCQSNYLQQGIDQLQTVIDTIKTNPESRRMIISSWNPKDIPLMVLPPCHTLCQFYVANGELSCQVYQRSGDMGLGVPFNIAGYALLTYIVAHVTGLKTGDLIHTMGDAHIYLNHIDALKVQLARSPKPFPCLKIIRNVTDINDFKWDDFQLDGYNPHPPL 295
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291    


Chain C from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhheeee.....eeeeeeeeeeeee.............hhhhhhhhhhhhhh....hhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.......eeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhhh......eeee.....hhhhhhhh.eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xsc C  15 LTGELQYLKQVDDILRYGVRKRDRTGIGTLSLFGMQARYNLRNEFPLLTTKRVFWRAVVEELLWFIRGSTDSKELAAKDIHIWDTGDLGPIYGFQWRHFGAEYKDCQSNYLQQGIDQLQTVIDTIKTNPESRRMIISSWNPKDIPLMVLPPCHTLCQFYVANGELSCQVYQRSGDMGLGVPFNIAGYALLTYIVAHVTGLKTGDLIHTMGDAHIYLNHIDALKVQLARSPKPFPCLKIIRNVTDINDFKWDDFQLDGYNPHPPL 295
                                    24        34        44        54        64        74        84        94   ||  121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291    
                                                                                                              98|                                                                                                                                                                                   
                                                                                                              116                                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh....hhhhhh..........hhhhhhh..............hhhhhhhh................hhhhhhhhhhhhh......eee...............eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhh........eeee..........hhh.eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xsc D  14 TLTGELQYLKQVDDILRYGVRKRDRTGIGTLSLFGMQARYNLRNEFPLLTTKRVFWRAVVEELLWFIRGSTDSKELAAKDIHIWDIYGSSKFLNRNGFHKRHTGDLGPIYGFQWRHFGAEYKDCQSNYLQQGIDQLQTVIDTIKTNPESRRMIISSWNPKDIPLMVLPPCHTLCQFYVANGELSCQVYQRSGDMGLGVPFNIAGYALLTYIVAHVTGLKTGDLIHTMGDAHIYLNHIDALKVQLARSPKPFPCLKIIRNVTDINDFKWDDFQLDGYNPHPPL 295
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
   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 4XSC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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        TYSY_VZVO | Q4JQW2: 4xsd 4xse

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