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 :  STRUCTURE OF BAMB FUSED TO A BAMA POTRA DOMAIN FRAGMENT
 
Authors :  K. B. Jansen, M. C. Sousa
Date :  13 May 14  (Deposition) - 10 Dec 14  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Bam Complex, Fusion, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. B. Jansen, S. L. Baker, M. C. Sousa
Crystal Structure Of Bamb Bound To A Periplasmic Domain Fragment Of Bama, The Central Component Of The Beta-Barrel Assembly Machine.
J. Biol. Chem. V. 290 2126 2015
PubMed-ID: 25468906  |  Reference-DOI: 10.1074/JBC.M114.584524

(-) Compounds

Molecule 1 - CHIMERA PROTEIN OF OUTER MEMBRANE PROTEIN ASSEMBLY FACTORS BAMA AND BAMB
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP P0A940 RESIDUES 175-424,UNP P77774 RESIDUES 21-392
    Gene: BAMA, YAET, YZZN, YZZY, B0177, JW0172, BAMB, YFGL, B2512, JW2496
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: OMP85

 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 4PK1)

(-) Sites  (0, 0)

(no "Site" information available for 4PK1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PK1)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Leu A:277 -Ala A:278
2Gln A:1041 -Phe A:1042
3Gly A:1114 -Val A:1115
4Gly A:1196 -Glu A:1197
5Asp A:1212 -Asn A:1213
6Glu A:1222 -Gln A:1223
7Val A:1254 -Asn A:1255
8Gly A:1265 -Asn A:1266

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PK1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PK1)

(-) Exons   (0, 0)

(no "Exon" information available for 4PK1)

(-) 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:494
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhh........hhhhhhhhhhhhhhhhh......eeeeeeee.......eeeeeeee.....eeeeeee................hhhhhhhhhhhhhhhhhhh......eeeeeeee....eeeeeeee..................eeeeee................ee..eeeee.....eeeee.....eeeee.......eeeeeeee..eeeeee...eeeeee.....eeeeee.................eee...eeeee......eeeeee.....ee.......ee...eeee.....eeeeee....eeeeeee.....eeeeee...eeeeee.....eeee.....eee...............eeeee.....eeeee.....eeeee...........eee..eeeee....eeeee......eeeeee..........eee..eeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4pk1 A  176 EIQQINIVGNHAFTTDELISHFQLRDEQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRMSPLPTVENQFTPTTAWSTSVGSGIGNFYSNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEPALLSGGVTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGAVKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQKVDSSGFQTEPVAADGKLLIQAKDGTVYSITR 1392
                                   185       195      |217       227       237       247       257       267       277       294       304       314       324       334       344 ||   1039      1049      1059      1069      1079      1089      1107      1117      1127      1137      1147      1157      1167      1177      1187      1197      1207      1217      1227     |1248      1258      1268      1278      1288      1298      1308      1318      1328      1338      1348      1358      1368      1378      1388    
                                                    202|                                                                    286|                                                 346|                                                              1098|                                                                                                                          1233|                                                                                                                                                   
                                                     215                                                                     294                                                 1032                                                               1107                                                                                                                           1245
   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 4PK1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PK1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PK1)

(-) Gene Ontology  (11, 17)

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 4pk1)
 
  Sites
(no "Sites" information available for 4pk1)
 
  Cis Peptide Bonds
    Asp A:1212 - Asn A:1213   [ RasMol ]  
    Gln A:1041 - Phe A:1042   [ RasMol ]  
    Glu A:1222 - Gln A:1223   [ RasMol ]  
    Gly A:1114 - Val A:1115   [ RasMol ]  
    Gly A:1196 - Glu A:1197   [ RasMol ]  
    Gly A:1265 - Asn A:1266   [ RasMol ]  
    Leu A:277 - Ala A:278   [ RasMol ]  
    Val A:1254 - Asn A:1255   [ 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
  4pk1
    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
  BAMA_ECOLI | P0A940
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  BAMB_ECOLI | P77774
    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
  BAMA_ECOLI | P0A940
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  BAMB_ECOLI | P77774
    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
        BAMA_ECOLI | P0A940: 2qcz 2qdf 2v9h 3efc 3og5 3q6b 4c4v 4n75 4xga 5ayw 5d0o 5d0q 5ekq 5ljo
        BAMB_ECOLI | P77774: 2yh3 2yms 3p1l 3prw 3q7m 3q7n 3q7o 4xga 5ayw 5d0o 5ljo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4PK1)