Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  POTRA1-2 OF THE PERIPLASMIC DOMAIN OF OMP85 FROM ANABAENA
 
Authors :  P. Koenig, E. Schleiff, I. Sinning, I. Tews
Date :  28 Mar 10  (Deposition) - 21 Apr 10  (Release) - 16 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Polypeptide Transport Associated, Potra, Outer Bacterial Membrane, Protein Membrane Transport, Beta Barrel Biogenesis, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Koenig, O. Mirus, R. Haarmann, M. S. Sommer, I. Sinning, E. Schleiff, I. Tews
Conserved Properties Of Polypeptide Transport-Associated (Potra) Domains Derived From Cyanobacterial Omp85.
J. Biol. Chem. V. 285 18016 2010
PubMed-ID: 20348103  |  Reference-DOI: 10.1074/JBC.M110.112649

(-) Compounds

Molecule 1 - ALR2269 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PERIPLASMIC POTRA DOMAINS (RESIDUES 161-467)
    Gene: ALR2269
    Organism Scientific: NOSTOC SP.
    Organism Taxid: 103690
    Strain: PCC 7120

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3MC9)

(-) Sites  (0, 0)

(no "Site" information available for 3MC9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MC9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MC9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MC9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MC9)

(-) Exons   (0, 0)

(no "Exon" information available for 3MC9)

(-) 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:161
 aligned with Q8YUR6_NOSS1 | Q8YUR6 from UniProtKB/TrEMBL  Length:833

    Alignment length:165
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376     
         Q8YUR6_NOSS1   217 TEPRVLVSEVLVRPQSGQLTPELETQVYNVIRTQPGRTTTRSQLQEDINAIFGTGFFSNVQASPEDTPLGVRVSFIVQPNPVLSKVEIQANPGTNVPSVLPQATADEIFRAQYGKILNLRDLQEGIKELTKRYQDQGYVLANVVGAPQVSENGVVTLQVAEGVVE 381
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee.....hhhhhhhhhhhh......eehhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeee.....eeeee...----......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.....ee....ee....eeeeeee..ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mc9 A 217 TEPRVLVSEVLVRPQSGQLTPELETQVYNVIRTQPGRTTTRSQLQEDINAIFGTGFFSNVQASPEDTPLGVRVSFIVQPNPVLSKVEIQANP----PSVLPQATADEIFRAQYGKILNLRDLQEGIKELTKRYQDQGYVLANVVGAPQVSENGVVTLQVAEGVVE 381
                                   226       236       246       256       266       276       286       296       306 |    |316       326       336       346       356       366       376     
                                                                                                                     308  313                                                                    


Chain B from PDB  Type:PROTEIN  Length:165
 aligned with Q8YUR6_NOSS1 | Q8YUR6 from UniProtKB/TrEMBL  Length:833

    Alignment length:165
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376     
         Q8YUR6_NOSS1   217 TEPRVLVSEVLVRPQSGQLTPELETQVYNVIRTQPGRTTTRSQLQEDINAIFGTGFFSNVQASPEDTPLGVRVSFIVQPNPVLSKVEIQANPGTNVPSVLPQATADEIFRAQYGKILNLRDLQEGIKELTKRYQDQGYVLANVVGAPQVSENGVVTLQVAEGVVE 381
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------Surf_Ag_VNR-3mc9B03 B:232-296                                    --POTRA_2-3mc9B01 B:299-378                                                       --- Pfam domains (1)
           Pfam domains (2) ---------------Surf_Ag_VNR-3mc9B04 B:232-296                                    --POTRA_2-3mc9B02 B:299-378                                                       --- Pfam domains (2)
         Sec.struct. author ....eeeeeeeeee.....hhhhhhhhhhhh......eehhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeee.....eeeeee............hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.....ee....ee....eeeeeee..ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mc9 B 217 TEPRVLVSEVLVRPQSGQLTPELETQVYNVIRTQPGRTTTRSQLQEDINAIFGTGFFSNVQASPEDTPLGVRVSFIVQPNPVLSKVEIQANPGTNVPSVLPQATADEIFRAQYGKILNLRDLQEGIKELTKRYQDQGYVLANVVGAPQVSENGVVTLQVAEGVVE 381
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376
   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 3MC9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MC9)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: POTRA (5)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8YUR6_NOSS1 | Q8YUR6)
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019867    outer membrane    The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

 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
(no "Ligands, Modified Residues, Ions" information available for 3mc9)
 
  Sites
(no "Sites" information available for 3mc9)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3mc9)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 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
  3mc9
    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
  Q8YUR6_NOSS1 | Q8YUR6
    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
  Q8YUR6_NOSS1 | Q8YUR6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8YUR6_NOSS1 | Q8YUR6: 3mc8

(-) Related Entries Specified in the PDB File

3mc8