Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A SEMISWEET
 
Authors :  Yan X. , Yuyong T. , Liang F. , K. Perry
Date :  17 Jun 14  (Deposition) - 10 Sep 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (2x)
Keywords :  Membrane Protein, Transporter (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Xu, Y. Tao, L. S. Cheung, C. Fan, L. Q. Chen, S. Xu, K. Perry, W. B. Frommer, L. Feng
Structures Of Bacterial Homologues Of Sweet Transporters In Two Distinct Conformations.
Nature V. 515 448 2014
PubMed-ID: 25186729  |  Reference-DOI: 10.1038/NATURE13670

(-) Compounds

Molecule 1 - CHEMICAL TRANSPORT PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PJEXPRESS411
    Gene: VIBRN418_06191
    Organism Scientific: VIBRIO SP. N418
    Organism Taxid: 701176

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1MYS2Ligand/IonPENTADECANE
2OLC3Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
3PE51Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1MYS4Ligand/IonPENTADECANE
2OLC6Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
3PE52Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1MYS4Ligand/IonPENTADECANE
2OLC6Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
3PE52Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:64 , LYS A:67 , OLC A:103 , OLC A:105BINDING SITE FOR RESIDUE MYS A 101
2AC2SOFTWAREPRO A:28 , THR A:47BINDING SITE FOR RESIDUE MYS A 102
3AC3SOFTWARETYR A:34 , LYS A:67 , LEU A:80 , ALA A:84 , VAL A:87 , MYS A:101 , OLC A:104BINDING SITE FOR RESIDUE OLC A 103
4AC4SOFTWARELEU A:20 , MET A:27 , TYR A:31 , VAL A:73 , LEU A:80 , OLC A:103BINDING SITE FOR RESIDUE OLC A 104
5AC5SOFTWAREILE A:90 , ALA A:91 , GLY A:94 , MYS A:101BINDING SITE FOR RESIDUE OLC A 105
6AC6SOFTWARESER A:22 , TYR A:52 , TRP A:59 , ASN A:75 , TYR A:82 , HOH A:234 , HOH A:237BINDING SITE FOR RESIDUE PE5 A 106

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QND)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QND)

(-) Sequences/Alignments

Asymmetric 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:97
                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                  4qnd A  1 MALIERIGKALEPLMLVMGLISPLATMPQLYKLYVSHSEHALGLSLTTWLLYSFIALLWTIYGIYHKNPTIWVGNCLGFLMYVAMVVGIIAHTGGTY 97
                                    10        20        30        40        50        60        70        80        90
   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 4QND)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    MYS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PE5  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4qnd)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4qnd
    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
  SWEET_VIBSN | F9RBV9
    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
  SWEET_VIBSN | F9RBV9
    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 4QND)

(-) Related Entries Specified in the PDB File

4qnc