Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  COMPLEX STRUCTURE OF THYMIDYLATE SYNTHASE FROM VARICELLA ZOSTER VIRUS WITH A DUMP
 
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, Viral Protein (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
    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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1UMP4Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:38 , 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 , ARG B:163 , ARG B:164binding site for residue UMP A 1001
2AC2SOFTWAREARG A:163 , ARG A:164 , CYS B:183 , GLN B:202 , ARG B:203 , GLY B:205 , ASP B:206 , ASN B:214 , HIS B:244 , TYR B:246 , HOH B:1101binding site for residue UMP B 1001
3AC3SOFTWAREARG C:38 , CYS C:183 , ARG C:203 , GLY C:205 , ASP C:206 , GLY C:210 , VAL C:211 , ASN C:214 , TYR C:246 , ARG D:163 , ARG D:164binding site for residue UMP C 1001
4AC4SOFTWAREARG C:163 , ARG C:164 , CYS D:183 , HIS D:184 , GLN D:202 , ARG D:203 , SER D:204 , GLY D:205 , ASP D:206 , ASN D:214 , HIS D:244 , TYR D:246binding site for residue UMP D 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XSD)

(-) 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...eeee.....eeeee..eeeeee.............hhhhhhhhhhhhhhh...hhhhhh...........hhhhhhhh.................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee.hhhhhhhhhh........eeee.....hhhhhhhh.eeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xsd A  15 LTGELQYLKQVDDILRYGVRKRDRTGIGTLSLFGMQARYNLRNEFPLLTTKRVFWRAVVEELLWFIRGSTDSKELAAKDIHIWGDLGPIYGFQWRHFGAEYKDCQSNYLQQGIDQLQTVIDTIKTNPESRRMIISSWNPKDIPLMVLPPCHTLCQFYVANGELSCQVYQRSGDMGLGVPFNIAGYALLTYIVAHVTGLKTGDLIHTMGDAHIYLNHIDALKVQLARSPKPFPCLKIIRNVTDINDFKWDDFQLDGYNPHPPL 295
                                    24        34        44        54        64        74        84        94  ||   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293  
                                                                                                             97|                                                                                                                                                                                  
                                                                                                             117                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhheeee...eeeee..eeeeee.............hhhhhhhhhhhhhh....hhhhhh..........hhhhhh..............hhhhhhhh..............hhhhhhhhhhhhh......eee...............eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhh.....................hhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xsd B  14 TLTGELQYLKQVDDILRYGVRKRDGIGTLSLFGMQARYNLRNEFPLLTTKRVFWRAVVEELLWFIRGSTDSKELAAKDIHIWDIYGSSKFLNRNGFHKRHTGDLGPIYGFQWRHFGAEYKSNYLQQGIDQLQTVIDTIKTNPESRRMIISSWNPKDIPLMVLPPCHTLCQFYVANGELSCQVYQRSGDMGLGVPFNIAGYALLTYIVAHVTGLKTGDLIHTMGDAHIYLNHIDALKVQLARSPKPFPCLKIIRNVTDINDFKWDDFQLDGYNPHPPL 295
                                    23        33   ||   45        55        65        75        85        95       105       115       125       135|      148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       
                                                  37|                                                                                            135|                                                                                                                                                            
                                                   40                                                                                             139                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.eeee.....eeeee..eeeeee..............hhhhhhhhhhhhh....hhhhhh............hhhhhhhh.................hhhhhhhhhhhhh......eee...............eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhh........eeee..............eeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xsd C  16 TGELQYLKQVDDILRYGVRKRDRTGIGTLSLFGMQARYNLRNEFPLLTTKRVFWRAVVEELLWFIRGSTDSKELAAKDIHIWDIDLGPIYGFQWRHFGAEYKDCQSNYLQQGIDQLQTVIDTIKTNPESRRMIISSWNPKDIPLMVLPPCHTLCQFYVANGELSCQVYQRSGDMGLGVPFNIAGYALLTYIVAHVTGLKTGDLIHTMGDAHIYLNHIDALKVQLARSPKPFPCLKIIRNVTDINDFKWDDFQLDGYNPHPPL 295
                                    25        35        45        55        65        75        85        95   ||  123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293  
                                                                                                              99|                                                                                                                                                                                 
                                                                                                              118                                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhheee.....eeee..eeeeee.............hhhhhhhhhhhhhh...............hhhhhhhhhhhhhh...........hhhhhhhh.................hhhhhhhhhhhhh......eee.................eeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhh........eeee..............eeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xsd D  14 TLTGELQYLKQVDDILRYGVRKRDGIGTLSLFGMQARYNLRNEFPLLTTKRVFWRAVVEELLWFIRGSTDSKELAAKDIHIWDIYGSSKFLNRNGFHKRHTGDLGPIYGFQWRHFGAEYKDCQSNYLQQGIDQLQTVIDTIKTNPESRRMIISSWNPKDIPLMVLPPCHTLCQFYVANGELSCQVYQRSGDMGLGVPFNIAGYALLTYIVAHVTGLKTGDLIHTMGDAHIYLNHIDALKVQLARSPKPFPCLKIIRNVTDINDFKWDDFQLDGYNPHPPL 295
                                    23        33   ||   45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295
                                                  37|                                                                                                                                                                                                                                                               
                                                   40
   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 4XSD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    UMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4xsd)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4xsd
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TYSY_VZVO | Q4JQW2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.45
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TYSY_VZVO | Q4JQW2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TYSY_VZVO | Q4JQW2: 4xsc 4xse

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4XSD)