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 :  STRUCTURE OF RECOMBINANT THAUMATIN IN THE PRESENCE OF 1.0M PST, PH7 AT 293K
 
Authors :  T. Masuda, K. Okubo, B. Mikami
Date :  26 Jan 15  (Deposition) - 03 Feb 16  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Thaumatin, Sweet-Tasting Protein, Sweet Receptor, Mainly Beta, Taste Protein, Sweet Taste Receptor, Aril, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Masuda, K. Okubo, B. Mikami
Structure Of The Recombinant Thaumatin In The Presence Of Pst At Room Temperature
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THAUMATIN I
    Chains: A
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Plasmid: PPIC6-PRE-TH
    Expression System Strain: X-33
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Organism Common: MIRACLE FRUIT
    Organism Scientific: THAUMATOCOCCUS DANIELLII
    Organism Taxid: 4621

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1TLA1Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:29 , GLU A:35 , SER A:36 , TYR A:157 , HOH A:405 , HOH A:406 , HOH A:525 , HOH A:535BINDING SITE FOR RESIDUE TLA A 301

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:9 -A:204
2A:56 -A:66
3A:71 -A:77
4A:121 -A:193
5A:126 -A:177
6A:134 -A:145
7A:149 -A:158
8A:159 -A:164

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:83 -Pro A:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3X3Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3X3Q)

(-) Exons   (0, 0)

(no "Exon" information available for 3X3Q)

(-) 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:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee....eeeeeeeee....eeeee.......eeeeeeeeeee.....eeeee..................eeeeeeee..eeeeeee........eeeee.......eee..hhhhhhhhhhh.......hhhhhhhhhhhhh.......hhhhhhhhhhh.............eeee....eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3x3q A   1 ATFEIVNRCSYTVWAAASKGDAALDAGGRQLNSGESWTINVEPGTNGGKIWARTDCYFDDSGSGICKTGDCGGLLRCKRFGRPPTTLAEFSLNQYGKDYIDISNIKGFNVPMDFSPTTRGCRGVRCAADIVGQCPAKLKAPGGGCNDACTVFQTSEYCCTTGKCGPTEYSRFFKRLCPDAFSYVLDKPTTVTCPGSSNYRVTFCPTA 207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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 3X3Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3X3Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3X3Q)

(-) Gene Ontology  (1, 1)

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
    TLA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:83 - Pro A:84   [ 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
  3x3q
    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
  A1IIJ1_THADA | A1IIJ1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  THM1_THADA | P02883
    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)
  (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
  A1IIJ1_THADA | A1IIJ1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  THM1_THADA | P02883
    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
        A1IIJ1_THADA | A1IIJ1: 2pe7 3x3o 3x3p 3x3r 3x3s 3x3t
        THM1_THADA | P02883: 1kwn 1lr2 1lr3 1lxz 1ly0 1pp3 1rqw 1thi 1thu 1thv 1thw 2a7i 2blr 2blu 2d8o 2d8p 2g4y 2oqn 2pe7 2vhk 2vhr 2vi1 2vi2 2vi3 2vi4 2vu6 2vu7 2wbz 3al7 3ald 3dzn 3dzp 3dzr 3e0a 3e3s 3n02 3n03 3qy5 3v7v 3v82 3v84 3v87 3v88 3v8a 3vce 3vcg 3vch 3vci 3vcj 3vck 3vhf 3vhg 3vjq 3x3o 3x3p 3x3r 3x3s 3x3t 3zej 4axr 4axu 4bal 4bar 4c3c 4dc5 4dc6 4diy 4diz 4dj0 4dj1 4ek0 4eka 4ekb 4ekh 4eko 4ekt 4el2 4el3 4el7 4ela 4tvt 4xvb 4zg3 4zxr 5a47 5amz 5avg 5fgt 5fgx 5jvx 5k7q 5kvw 5kvx 5kvz 5kw0 5kw3 5kw4 5kw5 5kw7 5kw8 5l4r 5lh0 5lh1 5lh3 5lh5 5lh6 5lh7 5lmh 5ln0 5t3g
UniProtKB/TrEMBL
        A1IIJ1_THADA | A1IIJ1: 3wxs

(-) Related Entries Specified in the PDB File

3al7 RECOMBINANT THAUMATIN I
3ald PLANT THAUMATIN I
3aok PLANT THAUMATIN II
3vhf PLANT THAUMATIN I
3wou RECOMBINANT THAUMATIN II
3wxs THAUMATIN (SFX)
3x3o
3x3p
3x3r
3x3s
3x3t