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 BAMD FROM E. COLI
 
Authors :  K. Zeth, R. Albrecht
Date :  28 Apr 11  (Deposition) - 01 Jun 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Lipoprotein, Essential Bam Component, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Albrecht, K. Zeth
Structural Basis Of Outer Membrane Protein Biogenesis In Bacteria.
J. Biol. Chem. V. 286 27792 2011
PubMed-ID: 21586578  |  Reference-DOI: 10.1074/JBC.M111.238931

(-) Compounds

Molecule 1 - UPF0169 LIPOPROTEIN YFIO
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 29-245
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 469008
    Synonym: BAMD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1URE1Ligand/IonUREA

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:173 , ASN A:176 , ARG A:177 , HOH A:2065BINDING SITE FOR RESIDUE URE A1234

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YHC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YHC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YHC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YHC)

(-) Exons   (0, 0)

(no "Exon" information available for 2YHC)

(-) 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:209
 aligned with BAMD_ECOLI | P0AC02 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:223
                                                                                                                                                                                                                                                245        
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    |    -   
           BAMD_ECOLI    31 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT--------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh--------------.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yhc A  11 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDD--------------DPQQARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNTLEHHHHHH 233
                                    20        30        40        50        60        70        80        90       100|        -     | 120       130       140       150       160       170       180       190       200       210       220       230   
                                                                                                                    101            116
   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 2YHC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YHC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YHC)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BAMD_ECOLI | P0AC02)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0043165    Gram-negative-bacterium-type cell outer membrane assembly    The assembly of an outer membrane of the type formed in Gram-negative bacteria. This membrane is enriched in polysaccharide and protein, and the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0051205    protein insertion into membrane    The process that results in the incorporation of a protein into a biological membrane. Incorporation in this context means having some part or covalently attached group that is inserted into the the hydrophobic region of one or both bilayers.
cellular component
    GO:1990063    Bam protein complex    Protein complex which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. In E. coli it is composed of BamABCDE, of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE. BamA interacts directly with BamB and the BamCDE subcomplex.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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
    URE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2yhc)
 

(-) 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
  2yhc
    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
  BAMD_ECOLI | P0AC02
    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
  BAMD_ECOLI | P0AC02
    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
        BAMD_ECOLI | P0AC02: 3q5m 3tgo 5ayw 5d0o 5d0q 5ekq 5ljo

(-) Related Entries Specified in the PDB File

2yh9 CRYSTAL STRUCTURE OF THE DIMERIC BAME FROM E. COLI