Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF C20S VARIANT OF DEHYDROASCORBATE REDUCTASE 3A FROM POPULUS TRICHOCARPA IN COMPLEX WITH DEHYDROASCORBIC ACID.
 
Authors :  T. Roret, P. Tsan
Date :  26 Jan 17  (Deposition) - 22 Mar 17  (Release) - 22 Mar 17  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Glutathione Transferase Dehydroascorbate Reductase Plant, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. A. Lallement, T. Roret, P. Tsan, J. M. Gualberto, J. M. Girardet, C. Didierjean, N. Rouhier, A. Hecker
Insights Into Ascorbate Regeneration In Plants: Investigating The Redox And Structural Properties Of Dehydroascorbate Reductases From Populus Trichocarpa.
Biochem. J. V. 473 717 2016
PubMed-ID: 26699905  |  Reference-DOI: 10.1042/BJ20151147

(-) Compounds

Molecule 1 - DEHYDROASCORBATE REDUCTASE FAMILY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: POPTR_0008S04920G
    Mutation: YES
    Organism Common: BLACK COTTONWOOD
    Organism Scientific: POPULUS TRICHOCARPA
    Organism Taxid: 3694
    Synonym: DEHYDROASCORBATE REDUCTASE 3A

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1UU31Ligand/Ion(5R)-5-[(1S)-1,2-BIS(OXIDANYL)ETHYL]OXOLANE-2,3,4-TRIONE
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1UU31Ligand/Ion(5R)-5-[(1S)-1,2-BIS(OXIDANYL)ETHYL]OXOLANE-2,3,4-TRIONE

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:19 , PRO A:21 , PHE A:22 , VAL A:107 , LEU A:110 , LYS A:111 , LYS A:156 , HIS A:159 , LYS A:209binding site for residue UU3 A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Val A:60 -Pro A:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MYE)

(-) Sequences/Alignments

NMR Structure
   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 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...........hhhhhhhhhhhhhh....eeeee.....hhhhh.........eeee..eee....hhhhhhhhh..........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mye A   1 MALEICVKAAVGAPNILGDSPFCQRVLLSLEEKKIPYKSHLINLGDKPQWFLEISPEGKVPVVKIDDKWVADSDVIVGILEEKNPEPPLATPPEFASVGSKIFPSFVKFLKSKDPNDGTEQALLEELKALDGHLKVHGPFIAGEKITAVDLSLAPKLYHLEVALGHFKNWPIPDNLTHVLNYIKLLFSRESFKKTRAAEEHVIAGWEPKVNA 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 5MYE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)

 Visualization

(-) Interactive Views

NMR Structure
  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
    UU3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:60 - Pro A:61   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - model 1, sites PNG format | NMR Structure - all models 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
  5mye
    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
  B9HM36_POPTR | B9HM36
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  B9HM36_POPTR | B9HM36
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B9HM36_POPTR | B9HM36: 2n5f 5n9u

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5MYE)