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 :  FLAVIN-DEPENDENT THYMIDYLATE SYNTHASE IN COMPLEX WITH FAD AND DEOXYURIDINE
 
Authors :  S. M. Bernard, F. W. Stull, J. L. Smith
Date :  08 Mar 16  (Deposition) - 08 Jun 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Fad-Dependent, Nucleotide Biosynthesis, Reductive Methylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. W. Stull, S. M. Bernard, A. Sapra, J. L. Smith, E. R. Zuiderweg, B. A. Palfey
Deprotonations In The Reaction Of Flavin-Dependent Thymidylate Synthase.
Biochemistry V. 55 3261 2016
PubMed-ID: 27214228  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00510

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE THYX
    Chains: A, B, C, D
    EC Number: 2.1.1.148
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: THYX, THY1, TM_0449
    Organism Scientific: THERMOTOGA MARITIMA (STRAIN ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
    Organism Taxid: 243274
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
    Synonym: TSASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1DUR4Ligand/Ion2'-DEOXYURIDINE
2FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3PGE10Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:78 , HIS A:79 , ARG A:80 , ILE A:81 , ASN A:169 , LEU A:173 , ARG A:174 , HIS A:178 , HOH A:411 , HOH A:420 , HOH A:427 , SER B:83 , ASN B:85 , GLU B:86 , SER B:88 , DUR B:303 , HOH B:430 , THR C:55 , GLU C:58 , ILE C:81 , ASN C:163 , ARG C:165 , FAD C:301 , PGE C:303binding site for residue FAD A 301
02AC2SOFTWAREGLY A:89 , ARG A:147 , THR A:156binding site for residue PGE A 302
03AC3SOFTWAREASN A:85 , FAD B:301 , HIS D:53 , THR D:55binding site for residue PGE A 303
04AC4SOFTWAREHIS A:43 , GLU A:46 , LYS A:50 , LEU D:215 , LYS D:216 , GLU D:217 , VAL D:218 , GLN D:219binding site for residue PGE A 304
05AC5SOFTWARELEU A:48 , GLY A:52 , HIS A:53 , PRO A:56 , HOH A:413 , LEU C:173 , FAD C:301 , ASN D:85binding site for residue PGE A 305
06AC6SOFTWAREARG A:74 , LEU A:152 , GLN A:180 , GLU B:86 , LEU B:87 , GLY B:89 , ARG B:90 , GLU B:144 , ARG B:147 , THR B:156binding site for residue PGE A 306
07AC7SOFTWAREASN A:85 , GLU A:86 , SER A:88 , PGE A:303 , HOH A:401 , HOH A:419 , ARG B:78 , HIS B:79 , ARG B:80 , ILE B:81 , ASN B:169 , LEU B:173 , ARG B:174 , HIS B:178 , DUR B:302 , HOH B:406 , HOH B:409 , HOH B:419 , HOH B:420 , HOH B:429 , THR D:55 , GLU D:58 , ILE D:81 , ASN D:163 , ARG D:165 , FAD D:301binding site for residue FAD B 301
08AC8SOFTWAREGLU A:86 , LEU A:87 , SER A:88 , GLY A:89 , ARG A:90 , ARG B:74 , GLN B:75 , ARG B:78 , ARG B:174 , FAD B:301 , HOH B:404binding site for residue DUR B 302
09AC9SOFTWAREGLN A:75 , ARG A:78 , ARG A:174 , FAD A:301 , GLU B:86 , LEU B:87 , SER B:88 , GLY B:89 , ARG B:90 , HOH B:408binding site for residue DUR B 303
10AD1SOFTWAREHIS B:43 , GLU B:46 , LYS B:50 , LEU C:215 , LYS C:216 , GLN C:219binding site for residue PGE B 304
11AD2SOFTWAREGLY B:52 , HIS B:53 , THR B:55 , HOH B:434 , ASN C:85 , FAD D:301binding site for residue PGE B 305
12AD3SOFTWARETHR A:55 , GLU A:58 , ILE A:81 , ASN A:163 , ARG A:165 , FAD A:301 , PGE A:305 , ARG C:78 , HIS C:79 , ARG C:80 , ILE C:81 , ASN C:169 , LEU C:173 , ARG C:174 , HIS C:178 , DUR C:302 , HOH C:428 , HOH C:437 , HOH C:444 , HOH C:446 , ASN D:85 , GLU D:86 , SER D:88binding site for residue FAD C 301
13AD4SOFTWAREARG C:74 , GLN C:75 , ARG C:78 , ARG C:174 , FAD C:301 , HOH C:409 , GLU D:86 , LEU D:87 , SER D:88 , GLY D:89 , ARG D:90binding site for residue DUR C 302
14AD5SOFTWAREFAD A:301 , GLY C:52 , HIS C:53 , GLU C:54 , ARG C:165 , HOH C:425binding site for residue PGE C 303
15AD6SOFTWAREGLU C:86 , LEU C:87 , GLY C:89 , ARG C:90 , GLU C:144 , ARG C:147 , THR C:156 , HOH C:403 , ARG D:74 , LEU D:152 , GLN D:180 , DUR D:302binding site for residue PGE C 304
16AD7SOFTWAREARG C:74 , LEU C:152 , GLN C:180 , HOH C:413 , GLU D:86 , LEU D:87 , GLY D:89 , GLU D:144 , ARG D:147 , THR D:156binding site for residue PGE C 305
17AD8SOFTWARETHR B:55 , GLU B:58 , ILE B:81 , ASN B:163 , ARG B:165 , FAD B:301 , PGE B:305 , HOH B:423 , ASN C:85 , GLU C:86 , SER C:88 , HOH C:405 , ARG D:78 , HIS D:79 , ARG D:80 , ILE D:81 , ASN D:169 , LEU D:173 , ARG D:174 , HIS D:178 , DUR D:302 , HOH D:411 , HOH D:418 , HOH D:422 , HOH D:434binding site for residue FAD D 301
18AD9SOFTWAREGLU C:86 , LEU C:87 , SER C:88 , GLY C:89 , ARG C:90 , PGE C:304 , ARG D:74 , GLN D:75 , ARG D:78 , ARG D:174 , FAD D:301 , HOH D:407binding site for residue DUR D 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IOQ)

(-) 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:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eeeeeeeee.hhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ioq A   0 HMKIDILDKGFVELVDVMGNDLSAVRAARVSFEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDIL 215
                                     9        19        29 ||     45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215
                                                          31|                                                                                                                                                                                 
                                                           38                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ioq B   1 MKIDILDKGFVELVDVMGNDLSAVRAARVSFDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDIL 215
                                    10        20        30 ||     45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215
                                                          32|                                                                                                                                                                                 
                                                           38                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeeeeee.hhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ioq C   0 HMKIDILDKGFVELVDVMGNDLSAVRAARVSFDLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQ 219
                                     9        19        29  ||    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        
                                                           32|                                                                                                                                                                                        
                                                            35                                                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeeeeee.hhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee...............hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ioq D   1 MKIDILDKGFVELVDVMGNDLSAVRAARVSDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQ 219
                                    10        20        30|       46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216   
                                                        30|                                                                                                                                                                                      
                                                         37
   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 5IOQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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
    DUR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGE  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
    AD9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5ioq)
 

(-) 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
  5ioq
    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
  THYX_THEMA | Q9WYT0
    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)
  2.1.1.148
    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
  THYX_THEMA | Q9WYT0
    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
        THYX_THEMA | Q9WYT0: 1kq4 1o24 1o25 1o26 1o27 1o28 1o29 1o2a 1o2b 3g4a 3g4c 3n0b 3n0c 4gt9 4gta 4gtb 4gtc 4gtd 4gte 4gtf 4gtl 4kar 4kas 4kat 5chp 5ior 5ios 5iot 5jfe

(-) Related Entries Specified in the PDB File

5ior 5ios 5iot