Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
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 :  ALTERNATIVE MODELS FOR TWO CRYSTAL STRUCTURES OF CANDIDA ALBICANS 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE-ALTERNATE INTERPREATION
 
Authors :  R. E. Stenkamp, I. Le Trong
Date :  12 Oct 07  (Deposition) - 29 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alternate Model, Magnesium, Manganese, Metal-Binding, Riboflavin Biosynthesis, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Le Trong, R. E. Stenkamp
Alternative Models For Two Crystal Structures Of Candida Albicans 3, 4-Dihydroxy-2-Butanone 4-Phosphate Synthase.
Acta Crystallogr. , Sect. D V. 64 219 2008
PubMed-ID: 18219123  |  Reference-DOI: 10.1107/S0907444907056132
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNCO-CARIB3-SYN
    Expression System Strain: XL1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RIB3
    Organism Scientific: CANDIDA ALBICANS
    Organism Taxid: 5476
    Synonym: DHBP SYNTHASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
15RP1Ligand/IonRIBULOSE-5-PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
15RP2Ligand/IonRIBULOSE-5-PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:34 , CYS A:59 , THR A:85 , LEU A:132 , ARG A:142 , GLY A:144 , HIS A:145 , THR A:146 , ILE A:164 , GLU A:166 , HOH A:773 , HOH A:798 , HOH A:814BINDING SITE FOR RESIDUE 5RP A 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RIU)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:125 -Pro A:126

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RIU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RIU)

(-) Exons   (0, 0)

(no "Exon" information available for 2RIU)

(-) 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:195
 aligned with RIB3_CANAL | Q5A3V6 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:201
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202 
           RIB3_CANAL     3 NIFTPIEEALEAYKNGEFLIVMDDEDRENEGDLIMAAELITQEKMAFLVRYSSGYVCVPLSEERANQLELPPMLANRSDRHGTAYTITCDFAEGTTTGISAHDRALTTRSLANPNSKPQDFIKPGHILPLRAVPGLLKKRRGHTEAAVQLSTLAGLQPAGVICELVRDEDGLMMRLDDCIQFGKKHGIKIININQLVEYIS 203
               SCOP domains d2riua_ A: automated matches                                                                                                                                                                              SCOP domains
               CATH domains 2riuA00 A:3-203 DHBP synthase                                                                                                                                                                             CATH domains
               Pfam domains -----DHBP_synthase-2riuA01 A:8-202                                                                                                                                                                      - Pfam domains
         Sec.struct. author ....hhhhhhhhhhh...eeee.........eeeee.hhhhhhhhhhhhhh.....eeeeehhhhhhh.......------.......eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeeee..hhhhh..hhhhhhhhhhhhh.....eeeee..........hhhhhhhhhhhhh..eeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2riu A   3 NIFTPIEEALEAYKNGEFLIVMDDEDRENEGDLIMAAELITQEKMAFLVRYSSGYVCVPLSEERANQLELPPMLA------GTAYTITCDFAEGTTTGISAHDRALTTRSLANPNSKPQDFIKPGHILPLRAVPGLLKKRRGHTEAAVQLSTLAGLQPAGVICELVRDEDGLMMRLDDCIQFGKKHGIKIININQLVEYIS 203
                                    12        22        32        42        52        62        72    |    - |      92       102       112       122       132       142       152       162       172       182       192       202 
                                                                                                     77     84
   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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: DHBP_synthase] (17)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (RIB3_CANAL | Q5A3V6)
molecular function
    GO:0008686    3,4-dihydroxy-2-butanone-4-phosphate synthase activity    Catalysis of the reaction: D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate + formate + H(+).
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009231    riboflavin biosynthetic process    The chemical reactions and pathways resulting in the formation of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).

 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
    5RP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:125 - Pro A:126   [ 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
  2riu
    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
  RIB3_CANAL | Q5A3V6
    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
  RIB3_CANAL | Q5A3V6
    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
        RIB3_CANAL | Q5A3V6: 1tks 1tku 2ris

(-) Related Entries Specified in the PDB File

1tku THE DATA SET FROM 1TKU WAS REINDEXED AND USED FOR REFINEMENT OF A MONOCLINIC MODEL.
2ris