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 :  CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA THIC WITH BOUND IMIDAZOLE RIBONUCLEOTIDE, S-ADENOSYLHOMOCYSTEINE, FE4S4 CLUSTER AND ZN (MONOCLINIC CRYSTAL FORM)
 
Authors :  M. K. Fenwick, A. P. Mehta, Y. Zhang, S. Abdelwahed, T. P. Begley, S. E. Ea
Date :  19 Jan 15  (Deposition) - 08 Apr 15  (Release) - 08 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Barrel, Radical Sam Superfamily, Iron-Sulfur Cluster, Thiamin, Vitamin B1, Vitamin B12, Domain Swapping, Adomet And Glutamate Mutase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Fenwick, A. P. Mehta, Y. Zhang, S. H. Abdelwahed, T. P. Begley, S. E. Ealick
Non-Canonical Active Site Architecture Of The Radical Sam Thiamin Pyrimidine Synthase.
Nat Commun V. 6 6480
PubMed-ID: 25813242  |  Reference-DOI: 10.1038/NCOMMS7480

(-) Compounds

Molecule 1 - PHOSPHOMETHYLPYRIMIDINE SYNTHASE, CHLOROPLASTIC
    Chains: A, B
    EC Number: 4.1.99.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 72-644
    Gene: THIC, PY
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: HYDROXYMETHYLPYRIMIDINE PHOSPHATE SYNTHASE, HMP-P SYNTHASE, HMP-PHOSPHATE SYNTHASE, HMPP SYNTHASE, PROTEIN PYRIMIDINE REQUIRING, THIAMINE BIOSYNTHESIS PROTEIN THIC, PROTEIN THIAMINE C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2IRN2Ligand/Ion1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1H-IMIDAZOLE
3SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4SF42Ligand/IonIRON/SULFUR CLUSTER
5ZN2Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:570 , MET A:572 , CYS A:573 , CYS A:578 , SER A:579 , MET A:580 , CL B:701 , SAH B:704BINDING SITE FOR RESIDUE SF4 A 701
02AC2SOFTWAREASN A:228 , MET A:257 , LEU A:259 , TYR A:286 , THR A:320 , HIS A:322 , SER A:342 , ARG A:343 , GLY A:344 , ASP A:383 , ARG A:386 , GLU A:422 , GLY A:423 , TYR A:449 , LEU A:451 , SAH A:703 , HOH A:919BINDING SITE FOR RESIDUE IRN A 702
03AC3SOFTWAREASN A:228 , ILE A:229 , GLY A:230 , LEU A:259 , VAL A:341 , ARG A:343 , ARG A:386 , HIS A:426 , GLU A:489 , HIS A:490 , LEU A:493 , PRO A:494 , IRN A:702 , ZN A:704 , HOH A:961 , HOH A:1006 , HOH A:1007 , HOH A:1008 , HOH A:1051 , HOH A:1065 , MET B:572 , CYS B:573 , SF4 B:702BINDING SITE FOR RESIDUE SAH A 703
04AC4SOFTWAREHIS A:426 , HIS A:490 , SAH A:703 , HOH A:961 , HOH A:962BINDING SITE FOR RESIDUE ZN A 704
05AC5SOFTWAREHIS A:490 , HOH A:963 , SF4 B:702BINDING SITE FOR RESIDUE CL A 705
06AC6SOFTWAREMET A:580 , SF4 A:701 , HIS B:490 , HOH B:1066BINDING SITE FOR RESIDUE CL B 701
07AC7SOFTWARESAH A:703 , CL A:705 , CYS B:570 , MET B:572 , CYS B:573 , CYS B:578 , SER B:579BINDING SITE FOR RESIDUE SF4 B 702
08AC8SOFTWAREASN B:228 , MET B:257 , LEU B:259 , TYR B:286 , THR B:320 , HIS B:322 , SER B:342 , ARG B:343 , GLY B:344 , ASP B:383 , ARG B:386 , GLU B:422 , GLY B:423 , TYR B:449 , LEU B:451 , SAH B:704BINDING SITE FOR RESIDUE IRN B 703
09AC9SOFTWAREMET A:572 , CYS A:573 , SF4 A:701 , ASN B:228 , ILE B:229 , GLY B:230 , LEU B:259 , VAL B:341 , ARG B:343 , ARG B:386 , HIS B:426 , LEU B:451 , GLU B:489 , HIS B:490 , LEU B:493 , PRO B:494 , IRN B:703 , ZN B:705 , HOH B:1008 , HOH B:1045 , HOH B:1054 , HOH B:1056 , HOH B:1057 , HOH B:1064BINDING SITE FOR RESIDUE SAH B 704
10BC1SOFTWAREHIS B:426 , HIS B:490 , SAH B:704 , HOH B:1064 , HOH B:1065BINDING SITE FOR RESIDUE ZN B 705

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4S26)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:424 -Gly A:425
2Gly A:452 -Pro A:453
3Pro B:424 -Gly B:425
4Gly B:452 -Pro B:453

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S26)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S26)

(-) Exons   (0, 0)

(no "Exon" information available for 4S26)

(-) 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:519
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhh..eeeeeeeee......eeeeeeeee........eee..................hhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhh..ee..............ee.....eeeeee.......hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh....eeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.eeee.......hhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhh...hhhhhhh..........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s26 A  77 PSSPDFQPIPSFEECFPKSTKEHKEVVHEESGHVLKVPFRRVHLSGGEPAFDNYDTSGPQNVNAHIGLAKLRKEWIDRREKLGTPRYTQMYYAKQGIITEEMLYCATREKLDPEFVRSEVARGRAIIPSNKKHLELEPMIVGRKFLVKVNANIGNSAVASSIEEEVYKVQWATMWGADTIMDLSTGRHIHETREWILRNSAVPVGTVPIYQALEKVDGIAENLNWEVFRETLIEQAEQGVDYFTIHAGVLLRYIPLTAKRLTGIVSRGGSIHAKWCLAYHKENFAYEHWDDILDICNQYDVALSIGDGLRPGSIYDANDTAQFAELLTQGELTRRAWEKDVQVMNEGPGHVPMHKIPENMQKQLEWCNEAPFYTLGPLTTDIAPGYDHITSAIGAANIGALGTALLCYVTPKEHLGLPNRDDVKAGVIAYKIAAHAADLAKQHPHAQAWDDALSKARFEFRWMDQFALSLDPMTAMSFHDETLPADGAKVAHFCSMCGPKFCSMKITEDIRKYAEENGY 595
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586         


Chain B from PDB  Type:PROTEIN  Length:512
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..eeeeeeeee......eeeeeeeee........eee..................hhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhh..ee..............ee.....eeeeee.......hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...eeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.eeee.......hhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhh...hhhhhhh..........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s26 B  84 PIPSFEECFPKSTKEHKEVVHEESGHVLKVPFRRVHLSGGEPAFDNYDTSGPQNVNAHIGLAKLRKEWIDRREKLGTPRYTQMYYAKQGIITEEMLYCATREKLDPEFVRSEVARGRAIIPSNKKHLELEPMIVGRKFLVKVNANIGNSAVASSIEEEVYKVQWATMWGADTIMDLSTGRHIHETREWILRNSAVPVGTVPIYQALEKVDGIAENLNWEVFRETLIEQAEQGVDYFTIHAGVLLRYIPLTAKRLTGIVSRGGSIHAKWCLAYHKENFAYEHWDDILDICNQYDVALSIGDGLRPGSIYDANDTAQFAELLTQGELTRRAWEKDVQVMNEGPGHVPMHKIPENMQKQLEWCNEAPFYTLGPLTTDIAPGYDHITSAIGAANIGALGTALLCYVTPKEHLGLPNRDDVKAGVIAYKIAAHAADLAKQHPHAQAWDDALSKARFEFRWMDQFALSLDPMTAMSFHDETLPADGAKVAHFCSMCGPKFCSMKITEDIRKYAEENGY 595
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593
   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 4S26)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S26)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S26)

(-) Gene Ontology  (11, 11)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IRN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SF4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:452 - Pro A:453   [ RasMol ]  
    Gly B:452 - Pro B:453   [ RasMol ]  
    Pro A:424 - Gly A:425   [ RasMol ]  
    Pro B:424 - Gly B:425   [ RasMol ]  
 

(-) 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
  4s26
    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
  THIC_ARATH | O82392
    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)
  4.1.99.17
    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
  THIC_ARATH | O82392
    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
        THIC_ARATH | O82392: 4n7q 4s25 4s27 4s28 4s29

(-) Related Entries Specified in the PDB File

3epm 3epn 3epo 4n7q 4s25 4s27 4s28 4s29 4s2a