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 :  STRUCTURAL INSIGHTS INTO THE REDUCTION MECHANISM OF SACCHAROMYCES CEREVISIA RIBOFLAVIN BIOSYNTHESIS REDUCTASE RIB7
 
Authors :  Z. Lv, J. Sun, Y. Liu
Date :  25 Sep 12  (Deposition) - 04 Sep 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Reductase, Nadph Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Lv, J. Sun, Y. Liu
Structural And Functional Insights Into Saccharomyces Cerevisiae Riboflavin Biosynthesis Reductase Rib7.
Plos One V. 8 61249 2013
PubMed-ID: 23620735  |  Reference-DOI: 10.1371/JOURNAL.PONE.0061249

(-) Compounds

Molecule 1 - 2,5-DIAMINO-6-RIBOSYLAMINO-4(3H)-PYRIMIDINONE 5'-PHOSPHATE REDUCTASE
    Chains: A, B
    EC Number: 1.1.1.302
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RIB7, YBR153W, YBR1203
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: DAROPP REDUCTASE, DARP REDUCTASE, 2,5-DIAMINO-6-(5-PHOSPHO- D-RIBOSYLAMINO)PYRIMIDIN-4(3H)-ONE REDUCTASE, 2,5-DIAMINO-6- RIBITYLAMINO-4(3H)-PYRIMIDINONE 5'-PHOSPHATE SYNTHASE, DARIPP SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:36 , ALA A:37 , VAL A:44 , GLY A:76 , SER A:77 , THR A:79 , ALA A:82 , THR A:107 , LYS A:108 , LEU A:158 , VAL A:159 , TRP A:161 , GLU A:180 , GLY A:182 , ALA A:183 , ASN A:184 , VAL A:185 , ILE A:186 , GLN A:188BINDING SITE FOR RESIDUE NDP A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HA9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro B:57 -Glu B:58

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HA9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HA9)

(-) Exons   (0, 0)

(no "Exon" information available for 4HA9)

(-) 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:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..........eeeeee...........hhhhhhhhhhh...eeeee.hhhhhh.........eeeee..........hhhhhhhhh......eeee...........eeee..........hhhhhhhhhhhhhh...eeeeehhhhhhhhh.......eeeeeee.ee...............eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ha9 A   8 EDLPQFLQNYLPNAGQTENTIVPFVTLTYAQSLDARVSRGHPETKTMTHYLRHHHDGILVGSGTVLADNPGLNCNSPRPIIIDTKQKWRFDGSKMQELFIKRQGKPPIVVVTSEPIIKEQHVDYAICPINDTTKLVDWKKLFEILKEEFNIRSVMVEGGANVINQLLLRSDIVNSLIITIGSTFLGSSGTEVSPPQTVNLKDMSWWKGITDVVLCARLA 242
                                    17        27        37        47|       65        75        85   ||  103       113       123       133       143       153       163       173       183       193       203       213       223       233         
                                                                  47|                               89|                                                                                                                                                
                                                                   56                                98                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:204
                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhh..............eeeeee..........hhhhhhhhhh...eeee...eeeee..........hhhhhhhhh......eeee...........eeee..........hhhhhhhhhhhhhh...eee..hhhhhhhhh.......eeeeeee................eeeeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ha9 B   8 EDLPQFLQNYLPNAGQTENTIVPFVTLTYAQSLDARVSRPETKTMTHYLRHHHDGILVNSPRPIIIDTKQKWRFDGSKMQELFIKRQGKPPIVVVTSEPIIKEQHVDYAICPINDTTKLVDWKKLFEILKEEFNIRSVMVEGGANVINQLLLRSDIVNSLIITIGSTFLGSSGTEVSPPQTVNLKDMSWWKGITDVVLCARLAD 243
                                    17        27        37        57        67       |99       109       119       129       139       149       159       169       179       189       199       209       219       229       239    
                                                                 46|                75|                                                                                                                                                 
                                                                  57                 98
   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 4HA9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HA9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HA9)

(-) 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
    NDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro B:57 - Glu B:58   [ 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
  4ha9
    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
  RIB7_YEAST | P33312
    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)
  1.1.1.302
    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
  RIB7_YEAST | P33312
    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
        RIB7_YEAST | P33312: 4ha7

(-) Related Entries Specified in the PDB File

4ha7