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 THE THE SLC26 TRANSPORTER SLC26DG IN COMPLEX WITH A NANOBODY
 
Authors :  R. Dutzler, E. R. Geertsma, Y. Chang, F. R. Shaik
Date :  19 Aug 15  (Deposition) - 09 Sep 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Membrane Transport Protein, Nanobody Complex, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. R. Geertsma, Y. N. Chang, F. R. Shaik, Y. Neldner, E. Pardon, J. Steyaert, R. Dutzler
Structure Of A Prokaryotic Fumarate Transporter Reveals The Architecture Of The Slc26 Family.
Nat. Struct. Mol. Biol. V. 22 803 2015
PubMed-ID: 26367249  |  Reference-DOI: 10.1038/NSMB.3091

(-) Compounds

Molecule 1 - SULPHATE TRANSPORTER
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DGEO_2773
    Organism Scientific: DEINOCOCCUS GEOTHERMALIS (STRAIN DSM 11300)
    Organism Taxid: 319795
 
Molecule 2 - NANOBODY
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: LLAMA
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1DMU2Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:131 , LEU A:240 , GLU A:241 , LEU A:244 , VAL A:335 , SER A:338 , THR A:339binding site for residue DMU A 601
2AC2SOFTWARETRP A:17 , ARG A:70 , PHE A:122 , ASP A:254 , THR A:255 , THR A:256 , PHE A:387binding site for residue DMU A 602

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:25 -B:99

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DA0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DA0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DA0)

(-) Exons   (0, 0)

(no "Exon" information available for 5DA0)

(-) 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:467
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee...hhhhhhhh........eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5da0 A  14 QREWFANPRKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISAATGAMALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNALAILIFMAQLPQFVGANWQMYAMVAAGLAIIYLLPLVFKAMPSALVAIVVLTVVAVVTGADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALTLSLVGLLESLLTAQLIDERTDTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVTSGGRGRLSTFVAGAFLMVLILALQPLLVQIPMAALVAVMMVVAISTFDWGSLRFPKGETVVMLATVAVTVFTHDLSLGVLIGVVLSALFFARKVSQLSQVTPVDEVDGTRTYRVRGQLFFVSTHDFLHQFDFTHPARRVVIDLSDAHFWDGSAVGALDKVMLKFMRQGTSVELRGLNAASATLVERL 484
                                    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       333       343  ||   357       367       377       387       397       407       417       427       437       447       457       467       477       
                                                                                                                                                                                                                                                                                                                                                                      346|                                                                                                                                     
                                                                                                                                                                                                                                                                                                                                                                       351                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.....eeeeee.....eeeeeee.....eeeeeeee....eeee........eeee.....eeeeee........eeeeee..............eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 5da0 B   9 ESGGGLVQAGGSLRLSCAASGSDVMGWFRQAPGKEREFVAAVTRSGGKSYNADSVKGRFTISRDNAKNTVSLQMNSLKPEDTAVYYCAAGDTAITSWYGYDYWGQGTQVTVS 124
                                    18        28||      42        52        62        72        82        92       102       112       122  
                                               29|                                                                                          
                                                34
   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 5DA0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DA0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DA0)

(-) Gene Ontology  (7, 7)

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
    DMU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5da0)
 

(-) 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
  5da0
    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
  Q1J2S8_DEIGD | Q1J2S8
    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
  Q1J2S8_DEIGD | Q1J2S8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q1J2S8_DEIGD | Q1J2S8: 5iof

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5DA0)