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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF CAULOBACTER CRESCENTUS THIC WITH FE4S4 CLUSTER AT REMOTE SITE (HOLO 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 :  2.93
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
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
    Chains: A
    EC Number: 4.1.99.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: THIC, CC_2029
    Organism Scientific: CAULOBACTER CRESCENTUS CB15
    Organism Taxid: 190650
    Strain: ATCC 19089 / CB15
    Synonym: HYDROXYMETHYLPYRIMIDINE PHOSPHATE SYNTHASE, HMP-P SYNTHASE, HMP-PHOSPHATE SYNTHASE, HMPP SYNTHASE, THIAMINE BIOSYNTHESIS PROTEIN THIC

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
2SF41Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
2SF42Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:322 , HIS A:347 , CYS A:561 , CYS A:564 , PHE A:568 , CYS A:569BINDING SITE FOR RESIDUE SF4 A 700
2AC2SOFTWARETYR A:277 , HIS A:313 , SER A:333 , ARG A:334 , GLY A:335 , ASP A:374 , ARG A:377BINDING SITE FOR RESIDUE PO4 A 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4S2A)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:415 -Gly A:416
2Gly A:443 -Pro A:444

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S2A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S2A)

(-) Exons   (0, 0)

(no "Exon" information available for 4S2A)

(-) 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:594
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeee.......eeeeeee..hhhhh...eeee..hhhhh...............hhhhhhhh..eee.......hhhhhh..hhhhh...........eee......hhhhhhh....hhhhhhhhhhhh........................hhhhhhhhhhh..ee..............ee.....eeeeee...hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh....eeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.eeee.............hhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhhh..eee...........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhh..........eee.hhhh..hhhhhhhhhhh...........hhhhhhhhhhhhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4s2a A  15 STGPIPGSRKVYQAGELFPELRVPFREVAVHPSANEPPVTIYDPSGPYSDPAIQIDIEKGLPRTREALVVARGDVEEVADPRQVKPEDNGFAQGKHLAPEFPDTGRKIYRAKPGKLVTQLEYARAGIITAEMEYVAIRENLRREQDRPCVRDGEDFGASIPDFVTPEFVRQEIARGRAIIPANINHGELEPMAIGRNFLVKINANIGNSTVADEVDKLVWATRWGADTVMDLSTGRNIHNIRDWIIRNSSVPIGTVPIYQALEKVNGVAEDLNWEVFRDTLIEQCEQGVDYFTIHAGVRLPFIPMTAKRVTGIVSRGGSIMAKWCLAHHKENFLYERFDEICEIMRAYDVSFSLGDGLRPGSTADANDEAQFSELRTLGELTKVAWKHGVQVMIEGPGHVAMHKIKANMDEQLKHCHEAPFYTLGPLTTDIAPGYDHITSAIGAAMIGWFGTAMLCYVTPKEHLGLPDRDDVKTGVITYKLAAHAADLAKGHPGAAMWDDAISRARFEFRWEDQFNLGLDPETARKFHDETLPKEAHKTAHFCSMCGPKFCSMKISQEVRDFAAGKAPNSAELGMAEMSEKFREQGSEIYLKTE 612
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608    
                                                                                                                                                                                                                                         222|                                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                                                                                                          227
   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 4S2A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S2A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S2A)

(-) 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
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SF4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:443 - Pro A:444   [ RasMol ]  
    Pro A:415 - Gly A:416   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  4s2a
    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_CAUCR | Q9A6Q5
    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_CAUCR | Q9A6Q5
    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_CAUCR | Q9A6Q5: 3epm 3epn 3epo

(-) Related Entries Specified in the PDB File

3epm 3epn 3epo 4n7q 4s25 4s26 4s27 4s28 4s29