Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - 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 :  CRYSTAL STRUCTURE OF PLASMODIUM VIVAX OROTIDINE 5-MONOPHOSPHATE DECARBOXYLASE WITH 6-AZA-UMP BOUND
 
Authors :  A. Dong, J. Lew, Y. Zhao, E. Sundararajan, G. Wasney, M. Vedadi, I. Koeie A. M. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, E. F. Pai, L. A. Bochkarev, R. Hui, M. Amani, Structural Genomics Consortium (S
Date :  01 May 06  (Deposition) - 16 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Odcase, 6-Aza-Ump, Structural Genomics, Structural Genomics Consortium, Sgc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dong, J. Lew, Y. Zhao, E. Sundararajan, G. Wasney, M. Vedadi, I. Koeieradzki, A. M. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, E. F. Pai, L. Kotra, A. Bochkarev, R. Hui, M. Amani
Crystal Structure Of Plasmodium Vivax Orotidine 5-Monophosphate Decarboxylase With 6-Aza-Ump Bound
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ODCASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P28-LIC-THROMBIN, PET28 DERIVED
    Expression System Strain: BL21 CODON PLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: MALARIA PARASITE P. VIVAX
    Organism Scientific: PLASMODIUM VIVAX
    Organism Taxid: 5855

 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
1UP61Ligand/Ion6-AZA URIDINE 5'-MONOPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1UP62Ligand/Ion6-AZA URIDINE 5'-MONOPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:41 , LYS A:133 , ASN A:135 , ASP A:167 , LYS A:169 , ASP A:172 , ILE A:173 , THR A:176 , THR A:225 , THR A:226 , PRO A:295 , GLN A:300 , GLY A:324 , ARG A:325 , HOH A:5204 , HOH A:5205 , HOH A:5221 , HOH A:5228 , HOH A:5249BINDING SITE FOR RESIDUE UP6 A 5203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GUU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GUU)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d2guua1 A:21-352 Protozoan orotidine monophosphate decarboxylase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhh..hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhh.....eeee.......hhhhhh.......eeeeeee.....hhhhhh..ee..eehhhhhhhhhhhhhhhh.hhhhh..eeeee...hhhhhhhhhhhh....eee........hhhhhhhhhh..hhh.eeeeehhhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2guu A  21 LKIKLQKRRDEVNTCLCIGLDPDEADIKSFMQSEKQNGYQSVKKNLSNSGELFAPQMGGQMLLAETPPKEAQEKDEFFYFFNHFCFYIINETKEYALAYKMNFAFYLPYGSLGVDVLKNVFDYLHHLNVPTILDIKMNDIGNTVKHYRKFIFDYLRSDSCTANIYMGTQMLRDICLDCKRYYSTFVLVKTTNADSHIFQNRLSLDGKEAYVVIAEEAQKMAKQLHLEENGEFVGFVVGANCYDEIKKIRELFPDCYILAPGVGAQKGDLRKMLCNGYSKNYEKVLINVGRAITKSGSPQQAAREYHQQIKEVLAELQ 352
                                    30        40        50        60        70|       93       103       113       123       133       143       153       163       173       183       193       203      |215       225       235       245       255       265       275       285       295       305       315       325       335       345       
                                                                            70|                                                                                                                           210|                                                                                                                                           
                                                                             84                                                                                                                            213
   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) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GUU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GUU)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2GUU)

 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
    UP6  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2guu)
 
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
  2guu
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 2GUU)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2GUU)