Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE CHLOROPLASTIC GAMMA-KETOL REDUCTASE FROM ARABIDOPSIS THALIANA
 
Authors :  S. Mas-Y-Mas, G. Curien, C. Giustini, N. Rolland, J. L. Ferrer, D. Cobes
Date :  03 Jun 15  (Deposition) - 28 Sep 16  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.34
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Gamma-Ketol Reductase, Arabidopsis Thaliana, Chloroplast, Oxydoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Mas Y Mas, G. Curien, C. Giustini, N. Rolland, J. L. Ferrer, D. Cobessi
Crystal Structure Of The Chloroplastic Oxoene Reductase Ceqorh From Arabidopsis Thaliana.
Front Plant Sci V. 8 329 2017
PubMed-ID: 28337214  |  Reference-DOI: 10.3389/FPLS.2017.00329

(-) Compounds

Molecule 1 - PUTATIVE QUINONE-OXIDOREDUCTASE HOMOLOG, CHLOROPLASTIC
    Chains: A, B
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: GAMMA-KETOL REDUCTASE
    Tissue: CHLOROPLAST

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5A3V)

(-) Sites  (0, 0)

(no "Site" information available for 5A3V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A3V)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Arg A:58 -Pro A:59
2Leu A:61 -Pro A:62
3Phe A:65 -Pro A:66
4Glu A:328 -Pro A:329
5Arg B:58 -Pro B:59
6Leu B:61 -Pro B:62
7Phe B:65 -Pro B:66
8Glu B:328 -Pro B:329

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A3V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A3V)

(-) Exons   (0, 0)

(no "Exon" information available for 5A3V)

(-) 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:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhheeeeee.......eeeeeeeeee.hhhhhhhhhh................eeeeeeeee...........eeeee.hhhh......eeeee...eee.....hhhhhhhhhhhhhhhhhhhhh.............eeeee...hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh...eeee..hhhhhhh.......eeeeee.....hhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a3v A   4 KLMHALQYNSYGGGAAGLEHVQVPVPTPKSNEVCLKLEATSLNPVDWKIQKGMIRPFLPRKFPCIPATDVAGEVVEVGSGVKNFKAGDKVVAVLSHLGGGGLAEFAVATEKLTVKRPQEVGAAEAAALPVAGLTALQALTNPAGLKLDGTGKKANILVTAASGGVGHYAVQLAKLANAHVTATCGARNIEFVKSLGADEVLDYKTPEGAALKSPSGKKYDAVVHCANGIPFSVFEPNLSENGKVIDITPGPNAMWTYAVKKITMSKKQLVPLLLIPKAENLEFMVNLVKEGKVKTVIDSKHPLSKAEDAWAKSIDGHATGKIIVEP 329
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323      


Chain B from PDB  Type:PROTEIN  Length:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhheeeeee.......eeeeeeeeee.hhhhhhhhhh................eeeeeeeee...........eeeee.hhhh......eeeee...eee.....hhhhhhhhhhhhhhhhhhhhh.............eeeee...hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh...eeee..hhhhhhh.......eeeeee.....hhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a3v B   3 GKLMHALQYNSYGGGAAGLEHVQVPVPTPKSNEVCLKLEATSLNPVDWKIQKGMIRPFLPRKFPCIPATDVAGEVVEVGSGVKNFKAGDKVVAVLSHLGGGGLAEFAVATEKLTVKRPQEVGAAEAAALPVAGLTALQALTNPAGLKLDGTGKKANILVTAASGGVGHYAVQLAKLANAHVTATCGARNIEFVKSLGADEVLDYKTPEGAALKSPSGKKYDAVVHCANGIPFSVFEPNLSENGKVIDITPGPNAMWTYAVKKITMSKKQLVPLLLIPKAENLEFMVNLVKEGKVKTVIDSKHPLSKAEDAWAKSIDGHATGKIIVEP 329
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322
   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 5A3V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A3V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A3V)

(-) Gene Ontology  (14, 14)

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
(no "Ligands, Modified Residues, Ions" information available for 5a3v)
 
  Sites
(no "Sites" information available for 5a3v)
 
  Cis Peptide Bonds
    Arg A:58 - Pro A:59   [ RasMol ]  
    Arg B:58 - Pro B:59   [ RasMol ]  
    Glu A:328 - Pro A:329   [ RasMol ]  
    Glu B:328 - Pro B:329   [ RasMol ]  
    Leu A:61 - Pro A:62   [ RasMol ]  
    Leu B:61 - Pro B:62   [ RasMol ]  
    Phe A:65 - Pro A:66   [ RasMol ]  
    Phe B:65 - Pro B:66   [ 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 ](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
  5a3v
    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
  QORH_ARATH | Q9SV68
    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.-.-.-
    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
  QORH_ARATH | Q9SV68
    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
        QORH_ARATH | Q9SV68: 5a3j 5a4d

(-) Related Entries Specified in the PDB File

5a3j CRYSTAL STRUCTURE OF THE CHLOROPLASTIC GAMMA-KETOL REDUCTASE FROM ARABIDOPSIS THALIANA BOUND TO 13-OXO-9 (Z),11(E),15(Z)- OCTADECATRIENOIC ACID.
5a4d CRYSTAL STRUCTURE OF THE CHLOROPLASTIC GAMMA-KETOL REDUCTASE FROM ARABIDOPSIS THALIANA BOUND TO 13KOTE AND NADP