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 OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH INHIBITOR BMP
 
Authors :  A. A. Fedorov, E. V. Fedorov, B. Desai, J. A. Gerlt, S. C. Almo
Date :  23 Sep 13  (Deposition) - 02 Oct 13  (Release) - 16 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.39
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel, Orotidine 5'-Monophosphate Decarboxylase, Inhibitor Bmp, Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, B. Desai, J. A. Gerlt, S. C. Almo
Crystal Structure Of Orotidine 5'-Monophosphate Decarboxylase From Archaeoglobus Fulgidus Complexed With Inhibitor Bmp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
    Chains: A, B
    EC Number: 4.1.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PYRF, AF_0929
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Synonym: OMP DECARBOXYLASE, OMPDCASE, OMPDECASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1BMP2Ligand/Ion6-HYDROXYURIDINE-5'-PHOSPHATE
2GOL2Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:29 , LYS A:51 , ASN A:53 , ASP A:77 , LYS A:79 , LEU A:133 , SER A:134 , PRO A:186 , GLN A:191 , GLY A:207 , ARG A:208 , HOH A:401 , HOH A:403 , HOH A:405 , HOH A:413 , HOH A:415 , ASP B:82 , VAL B:83 , THR B:86BINDING SITE FOR RESIDUE BMP A 301
2AC2SOFTWARESER A:135 , GLN A:191 , ARG A:208 , HOH A:426 , HOH A:550 , PRO B:84 , TYR B:85BINDING SITE FOR RESIDUE GOL A 302
3AC3SOFTWAREASP A:82 , VAL A:83 , THR A:86 , ASP B:29 , LYS B:51 , ASN B:53 , ASP B:77 , LYS B:79 , LEU B:133 , SER B:134 , PRO B:186 , GLN B:191 , GLY B:207 , ARG B:208 , HOH B:401 , HOH B:402 , HOH B:404 , HOH B:409 , HOH B:411BINDING SITE FOR RESIDUE BMP B 301
4AC4SOFTWAREVAL A:83 , PRO A:84 , TYR A:85 , SER B:135 , GLN B:191 , ARG B:208 , HOH B:421 , HOH B:582BINDING SITE FOR RESIDUE GOL B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MUZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MUZ)

(-) 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:212
                                                                                                                                                                                                                                                    
               SCOP domains d4muza_ A: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....hhhhhhhhhhhhhhhh.eeeeehhhhhhhh.hhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhh..eeee........hhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4muz A  18 GSHMKQLILALDVMDGEKAMEIAKKVAEHVDRIKVNYPLVLSAGVGIMKRLSEIKPVIADFKIADVPYTSSLIARIAFENSAESVIVHGFVGSDTLREVCRVAEEFGGKVYAVTELSSPGGEEFMSAVSLKIVEKAKEAGCHGLIAPSTRIERLREIRKAAGDMEILCPGIGAQKGSIEAVKYADGIIVGRGIYASGNPAEEARKLRRVLKI 229
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227  


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d4muzb_ B: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....hhhhhhhhhhhhhhhh.eeeeehhhhhhhh.hhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhh..eeee........hhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4muz B  18 GSHMKQLILALDVMDGEKAMEIAKKVAEHVDRIKVNYPLVLSAGVGIMKRLSEIKPVIADFKIADVPYTSSLIARIAFENSAESVIVHGFVGSDTLREVCRVAEEFGGKVYAVTELSSPGGEEFMSAVSLKIVEKAKEAGCHGLIAPSTRIERLREIRKAAGDMEILCPGIGAQKGSIEAVKYADGIIVGRGIYASGNPAEEARKLRRVLKI 229
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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
    BMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4muz)
 

(-) 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
  4muz
    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
  PYRF_ARCFU | O29333
    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)
  4.1.1.23
    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
  PYRF_ARCFU | O29333
    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
        PYRF_ARCFU | O29333: 4n2y

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4MUZ)