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 BOVINE FRUCTOSE TRANSPORTER GLUT5 IN AN OPEN INWARD-FACING CONFORMATION
 
Authors :  G. Verdon, H. J. Kang, S. Iwata, D. Drew
Date :  18 Feb 15  (Deposition) - 14 Oct 15  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  D
Keywords :  Glut5 Transporter, Fructose, Bovine Mfs, Open Inward-Facing Conformation, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Nomura, G. Verdon, H. J. Kang, T. Shimamura, Y. Nomura, Y. Sonoda, S. A. Hussien, A. A. Qureshi, M. Coincon, Y. Sato, H. Abe, Y. Nakada-Nakura, T. Hino, T. Arakawa, O. Kusano-Arai, H. Iwanari, T. Murata, T. Kobayashi, T. Hamakubo, M. Kasahara, S. Iwata, D. Drew
Structure And Mechanism Of The Mammalian Fructose Transporter Glut5.
Nature V. 526 397 2015
PubMed-ID: 26416735  |  Reference-DOI: 10.1038/NATURE14909

(-) Compounds

Molecule 1 - SOLUTE CARRIER FAMILY 2, FACILITATED GLUCOSE TRANSPORTER MEMBER 5
    Chains: D
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Taxid: 4932
    Gene: SLC2A5, GLUT5
    Mutation: YES
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: FRUCTOSE TRANSPORTER,GLUCOSE TRANSPORTER TYPE 5,SMALL INTESTINE,GLUT-5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4YB9)

(-) Sites  (0, 0)

(no "Site" information available for 4YB9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YB9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr D:360 -Gly D:361
2Ile D:369 -Ser D:370

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YB9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YB9)

(-) Exons   (0, 0)

(no "Exon" information available for 4YB9)

(-) 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 D from PDB  Type:PROTEIN  Length:437
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yb9 D  19 LATLIAAFGSSFQYGYNVAAINSPSEFMKDFYAYTYYDRVGEYMNEFYLTLLWSVTVSMFPFGGFLGSLMVGPLVNNLGRKGTLLFNNIFSIVPALLMGFSELAKSFEMIIVARVLVGICAGLSSNVVPMYLGELAPKNWRGALGVVPQLFITIGILVAQIFGLRSLLANEEGWPILLGLTGIPAVLQLLFLPFFPESPRYLLIQKKDEAAAKSALRRLAEIEEILEEDRAEKAVGFISVLKLFKMRSLRWQVISIIVLMAGQQLSGVNAIYYYADQIYLSAGVNEDDVQYVTAGTGAVNVLITVCAIFVVELMGRRFLLLLGFSVCFTACCVLTGALALQDVISWMPYVSIACVISYVIGHALGPSPIPALLVTEIFLQSSRPAAYMVAGTVHWLSNFTVGLVFPFIQVGLGAYSFVIFAVICLLTTVYIFLIIPE 462
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       
                                                                                                                                                                                                                                                    237|                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                     245
   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 4YB9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YB9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YB9)

(-) Gene Ontology  (19, 19)

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 4yb9)
 
  Sites
(no "Sites" information available for 4yb9)
 
  Cis Peptide Bonds
    Ile D:369 - Ser D:370   [ RasMol ]  
    Thr D:360 - Gly D:361   [ 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
  4yb9
    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
  GTR5_BOVIN | P58353
    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
  GTR5_BOVIN | P58353
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4YB9)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4YB9)