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

(-) Description

Title :  MOLECULAR STRUCTURE OF AN APOLIPOPROTEIN DETERMINED AT 2.5-ANGSTROMS RESOLUTION
 
Authors :  H. Holden
Date :  30 Nov 92  (Deposition) - 31 Jan 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Lipoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. R. Breiter, M. R. Kanost, M. M. Benning, G. Wesenberg, J. H. Law, M. A. Wells, I. Rayment, H. M. Holden
Molecular Structure Of An Apolipoprotein Determined At 2. 5-A Resolution.
Biochemistry V. 30 603 1991
PubMed-ID: 1988048  |  Reference-DOI: 10.1021/BI00217A002
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - APOLIPOPHORIN III
    Chains: A
    Engineered: YES
    Organism Common: MIGRATORY LOCUST
    Organism Scientific: LOCUSTA MIGRATORIA
    Organism Taxid: 7004

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1AEP)

(-) Sites  (0, 0)

(no "Site" information available for 1AEP)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1AEP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1AEP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AEP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1AEP)

(-) Exons   (0, 0)

(no "Exon" information available for 1AEP)

(-) 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:153
 aligned with APL3_LOCMI | P10762 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:153
                                                                                                                                            138                                      
                                                                                                                                          137 |                                      
                                    34        44        54        64        74        84        94       104       114       124       134  | |  143       153       163       173   
           APL3_LOCMI    25 NIAEAVQQLNHTIVNAAHELHETLGLPTPDEALNLLTEQANAFKTKIAEVTTSLKQEAEKHQGSVAEQLNRFARNLNNSIHDAATSAQPADQLNSLQSALTNVGHQWQTSQPR-PSVAQEAWAPVQSALQEAAEKTKEAAANLQNSIQSAVQK 176
               SCOP domains d1aepa_ A: Apolipophorin-III                                                                                                                              SCOP domains
               CATH domains 1aepA00 A:6-158 Apolipoprotein (APOA1 / APOA4 / APOE FAMILY)                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1aep A   6 NIAEAVQQLNHTIVNAAHELHETLGLPTPDEALNLLTEQANAFKTKIAEVTTSLKQEAEKHQGSVAEQLNAFARNLNNSIHDAATSLNLQDQLNSLQSALTNVGHQWQDIATKTQASAQEAWAPVQSALQEAAEKTKEAAANLQNSIQSAVQK 158
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AEP)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (APL3_LOCMI | P10762)
biological process
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 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 1aep)
 
  Sites
(no "Sites" information available for 1aep)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1aep)
 

(-) 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)
Midas
  ribbon, secondary structure
[ mono GIF format | stereo GIF format ]
  ribbon, secondary structure
[ mono GIF format | stereo GIF format ]
  sticks
[ mono GIF format | stereo GIF format ]
  spacefill
[ mono GIF format | stereo GIF format ]
Setor
  ribbon, labeling
[ mono GIF format | stereo GIF format ]
  ribbon, secondary structure, labeling
[ mono GIF format | stereo GIF format ]
  ribbon, secondary structure, labeling, sidechains
[ mono GIF format | stereo GIF format ]
  spacefill
[ mono GIF format | stereo GIF format ]
Distance Plot
  representative atom: CA
[ mono GIF format | mono PDF format ]

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1aep
    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
  APL3_LOCMI | P10762
    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
  APL3_LOCMI | P10762
    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
        APL3_LOCMI | P10762: 1ls4

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1AEP)