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 :  RAT PRESTIN STAS DOMAIN IN COMPLEX WITH IODIDE
 
Authors :  G. Lolli, E. Pasqualetto, E. Costanzi, G. Bonetto, R. Battistutta
Date :  19 Nov 15  (Deposition) - 16 Dec 15  (Release) - 17 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Anion-Binding Site, Protein-Anion Complex, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Lolli, E. Pasqualetto, E. Costanzi, G. Bonetto, R. Battistutta
The Stas Domain Of Mammalian Slc26A5 Prestin Harbours An Anion-Binding Site.
Biochem. J. V. 473 365 2016
PubMed-ID: 26635354  |  Reference-DOI: 10.1042/BJ20151089
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PRESTIN,PRESTIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET SUMO
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: STAS DOMAIN,STAS DOMAIN
    Gene: SLC26A5, PRES
    Mutation: YES
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: RESIDUES 564-636 (VARIABLE LOOP) ARE DELETED, GLYSER ARE INSERTED BETWEEN POSITION 563 AND 637. MET651SEMET
    Synonym: SOLUTE CARRIER FAMILY 26 MEMBER 5,SOLUTE CARRIER FAMILY 26 MEMBER 5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2IOD4Ligand/IonIODIDE ION
3MSE1Mod. Amino AcidSELENOMETHIONINE
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:714binding site for residue IOD A 801
02AC2SOFTWAREGLN A:648 , ALA A:718binding site for residue IOD A 803
03AC3SOFTWAREILE A:706binding site for residue IOD A 804
04AC4SOFTWAREGLN A:513 , VAL A:710binding site for residue EDO A 805
05AC5SOFTWARELYS A:536binding site for residue EDO A 806
06AC6SOFTWARETHR A:688 , LYS A:699binding site for residue EDO A 807
07AC7SOFTWAREASN A:638 , SER A:680 , ALA A:681 , GLN A:682binding site for residue EDO A 808
08AC8SOFTWAREGLY A:534 , ASN A:638 , GLN A:682binding site for residue EDO A 809
09AC9SOFTWAREGLY A:668 , TYR A:673 , ALA A:718binding site for residue PGE A 810
10AD1SOFTWAREASP A:518 , ASP A:522binding site for residue PEG A 811
11AD2SOFTWAREPRO A:506 , ALA A:542 , ASN A:695binding site for residue PEG A 812

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EUZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EUZ)

(-) 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:130
                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee......eee............eeeeee..hhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh....hhhhhh.ee.hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5euz A 505 SPSYTVLGQLPDTDVYIDIDAYEEVKEIPGIKIFQINAPIYYANSDLYENIHTVILDFTQVNFmDSVGVKTLAGIVKEYGDVGIYVYLAGCSAQVVNDLTSNRFFENPALKELLFHSIHDAVLGSQVREA 718
                                   514       524       534       544       638       648   |   658       668       678       688       698       708       718
                                                                         552|            652-MSE                                                              
                                                                          637
   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 5EUZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (42, 42)

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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IOD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5euz)
 

(-) 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
  5euz
    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
  S26A5_RAT | Q9EPH0
    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
  S26A5_RAT | Q9EPH0
    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
        S26A5_RAT | Q9EPH0: 3llo 5eus 5euu 5euw 5eux

(-) Related Entries Specified in the PDB File

3llo 3LLO CONTAINS THE SAME PROTEIN IN THE APO FORM
5eus 5EUS CONTAINS THE SAME PROTEIN IN COMPLEX WITH BROMIDE
5euu 5EUU CONTAINS THE SAME PROTEIN IN COMPLEX WITH CHLORIDE
5euw 5EUW CONTAINS THE SAME PROTEIN IN COMPLEX WITH NITRATE
5eux 5EUX CONTAINS THE SAME PROTEIN IN COMPLEX WITH THIOCYANATE