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

(-) Description

Title :  MOUSE THYMIDYLATE SYNTHASE IN TERNARY COMPLEX WITH FDUMP AND METHYLENETETRAHYDROFOLATE.
 
Authors :  A. Dowiercial, P. Wilk, A. Jarmula, W. Rode
Date :  15 Dec 15  (Deposition) - 26 Oct 16  (Release) - 26 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Complex, Enzyme, Inhibitor, Cofactor, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dowiercial, A. Jarmula, P. Wilk, W. Rypniewski, M. Kowalska, T. Fraczyk, J. Ciesla, W. Rode
Mouse Thymidylate Synthase Does Not Show The Inactive Conformation, Observed For The Human Enzyme
Struct Chem 2016
PubMed: search  |  Reference-DOI: 10.1007/S11224-016-0840-8

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TYMS, MCG_11630
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: THYMIDYLATE SYNTHASE,ISOFORM CRA_B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1C2F2Ligand/Ion5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID
2UFP2Ligand/Ion5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:44 , TRP A:103 , TYR A:129 , CYS A:189 , HIS A:190 , GLN A:208 , ARG A:209 , SER A:210 , GLY A:211 , ASP A:212 , ASN A:220 , HIS A:250 , TYR A:252 , C2F A:402 , HOH A:569 , HOH A:675 , HOH A:708 , ARG B:169 , ARG B:170binding site for residue UFP A 401
2AC2SOFTWAREPHE A:74 , ILE A:102 , TRP A:103 , ASN A:106 , LEU A:186 , ASP A:212 , LEU A:215 , GLY A:216 , MET A:305 , ALA A:306 , UFP A:401 , HOH A:506 , HOH A:514 , HOH A:558 , HOH A:575 , HOH A:590 , HOH A:636 , HOH A:644 , HOH A:647 , HOH A:667 , HOH A:670 , HOH A:701binding site for residue C2F A 402
3AC3SOFTWAREARG A:169 , ARG A:170 , ARG B:44 , LYS B:71 , ARG B:72 , VAL B:73 , PHE B:74 , ILE B:102 , TRP B:103 , ASN B:106 , TYR B:129 , LEU B:186 , CYS B:189 , HIS B:190 , GLN B:208 , ARG B:209 , SER B:210 , GLY B:211 , ASP B:212 , LEU B:215 , GLY B:216 , PHE B:219 , ASN B:220 , HIS B:250 , TYR B:252 , ILE B:301 , MET B:303 , MET B:305 , ALA B:306 , HOH B:505 , HOH B:512 , HOH B:534 , HOH B:561 , HOH B:601 , HOH B:608 , HOH B:610 , HOH B:616 , HOH B:618 , HOH B:619 , HOH B:626 , HOH B:672binding site for residues UFP B 401 and C2F B 402
4AC4SOFTWAREARG A:169 , ARG A:170 , ARG B:44 , LYS B:71 , ARG B:72 , VAL B:73 , PHE B:74 , ILE B:102 , TRP B:103 , ASN B:106 , TYR B:129 , LEU B:186 , CYS B:189 , HIS B:190 , GLN B:208 , ARG B:209 , SER B:210 , GLY B:211 , ASP B:212 , LEU B:215 , GLY B:216 , PHE B:219 , ASN B:220 , HIS B:250 , TYR B:252 , ILE B:301 , MET B:303 , MET B:305 , ALA B:306 , HOH B:505 , HOH B:512 , HOH B:534 , HOH B:561 , HOH B:601 , HOH B:608 , HOH B:610 , HOH B:616 , HOH B:618 , HOH B:619 , HOH B:626 , HOH B:672binding site for residues UFP B 401 and C2F B 402
5AC5SOFTWAREARG A:169 , ARG A:170 , ARG B:44 , TRP B:103 , TYR B:129 , PRO B:187 , PRO B:188 , HIS B:190 , ALA B:191 , GLN B:208 , ARG B:209 , SER B:210 , GLY B:211 , ASP B:212 , ASN B:220 , HIS B:250 , TYR B:252 , C2F B:402 , HOH B:601 , HOH B:616 , HOH B:672binding site for Di-peptide UFP B 401 and CYS B 189

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FCT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FCT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FCT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FCT)

(-) Exons   (0, 0)

(no "Exon" information available for 5FCT)

(-) 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:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh...hhhhhhh......hhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fct A  21 RHGELQYLRQVEHILRCGFKKEDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVRIWDANGSRDFLDSLGFSARQEGDLGPVYGFQWRHFGAEYKDMDSDYSGQGVDQLQKVIDTIKTNPDDRRIIMCAWNPKDLPLMALPPCHALCQFYVVNGELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLQPGDFVHTLGDAHIYLNHIEPLKIQLQREPRPFPKLKILRKVETIDDFKVEDFQIEGYNPHPTIKMEMAV 307
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       


Chain B from PDB  Type:PROTEIN  Length:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.....hhhhhhhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fct B  21 RHGELQYLRQVEHILRCGFKKEDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVRIWDANGSRDFLDSLGFSARQEGDLGPVYGFQWRHFGAEYKDMDSDYSGQGVDQLQKVIDTIKTNPDDRRIIMCAWNPKDLPLMALPPCHALCQFYVVNGELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLQPGDFVHTLGDAHIYLNHIEPLKIQLQREPRPFPKLKILRKVETIDDFKVEDFQIEGYNPHPTIKMEMAV 307
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
   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 5FCT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FCT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FCT)

(-) Gene Ontology  (42, 79)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    C2F  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UFP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5fct)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  5fct
    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
  Q544L2_MOUSE | Q544L2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TYSY_MOUSE | P07607
    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)
  (no 'Enzyme Classificator' available)
    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
  Q544L2_MOUSE | Q544L2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TYSY_MOUSE | P07607
    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_MOUSE | P07607: 3ihi 4e5o 4eb4 4ein 4ez8

(-) Related Entries Specified in the PDB File

3ihi 3IHI CONTAINS THE SAME PROTEIN WITHOUT LIGANDS.
4e50 4E50 CONTAINS THE SAME PROTEIN COMPLEXED WITH DUMP.
4eb4 4EB4 CONTAINS THE SAME PROTEIN COMPLEXED WITH DUMP AND TOMUDEX.
4ein 4EIN CONTAINS THE SAME PROTEIN COMPLEXED WITH N(4)-HYDROXY-2'- DEOXYCYTIDINE-5'-MONOPHOSPHATE.
4ez8 4EZ8 CONTAINS THE SAME PROTEIN COMPLEXED WITH N(4)-HYDROXY-2'- DEOXYCYTIDINE-5'-MONOPHOSPHATE AND DIHYDROFOLATE.