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 :  CRYSTAL STRUCTURE OF PUTATIVE OUTER MEMBRANE LIPOPROTEIN-SORTING PROTEIN DOMAIN FROM VIBRIO PARAHAEMOLYTICUS
 
Authors :  R. Wu, J. Abdullah, A. Joachimiak, Midwest Center For Structural G (Mcsg)
Date :  05 Dec 07  (Deposition) - 05 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Putative Outer Membrane Protein Domain, Psi-2, Protein Structure Initiative, Structural Genomics, Midwest Center For Structural Genomics (Mcsg), Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Wu, J. Abdullah, A. Joachimiak
The Crystal Structure Of Putative Outer Membrane Lipoprotein-Sorting Protein Domain From Vibrio Parahaemolyticus.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE OUTER MEMBRANE LIPOPROTEIN-SORTING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 28-261
    Gene: VP1287
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS RIMD 2210633
    Organism Taxid: 223926

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:2 , HIS A:125 , LYS A:127 , ASP A:128BINDING SITE FOR RESIDUE MG A 235

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BK5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:60 -Pro A:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BK5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BK5)

(-) Exons   (0, 0)

(no "Exon" information available for 3BK5)

(-) 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:235
 aligned with Q87Q63_VIBPA | Q87Q63 from UniProtKB/TrEMBL  Length:263

    Alignment length:236
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255      
         Q87Q63_VIBPA    26 NEEKGLEIAQERKARDEGWGDSIATMEMILKNAQGESSTRLMRLKSLEVEGDGDKGLTIFDQPRDVTGTAFLNHSHTIGADDQWLYLPALKRVKRISSRNKSGPFMGSEFAYEDLSSFEIEKYRFNHLKDEKFNGQDVFVLEQIPTDKNSGYTKQVVWLDKAHYRPLKVEFYDRKGALLKTLTFANYKQYLDKYWRAHTMAMTNHQTGKSTELNTSDLRFQTGLEENDFNKNVLKR 261
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bk5A00 A:-1-234 outer membrane li poprotein receptor (LolB), chain A                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.....eeeeeeeeeee...-..eeeeeeeeee.......eeeeeeee.......eeeee.......eeeeee....eeee.hhhhh.........hhhhhh..hhh.eeeeeeeeeee..eeeeeeeeee......eeeeeeeee.....eeeeeeee....eeeeeeeeeeeee...eeeeeeeeeee.....eeeeeeeeeee....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bk5 A  -1 NAEKGLEIAQERKARDEGWGDSIATmEmILKNAQ-ESSTRLmRLKSLEVEGDGDKGLTIFDQPRDVTGTAFLNHSHTIGADDQWLYLPALKRVKRISSRNKSGPFmGSEFAYEDLSSFEIEKYRFNHLKDEKFNGQDVFVLEQIPTDKNSGYTKQVVWLDKAHYRPLKVEFYDRKGALLKTLTFANYKQYLDKYWRAHTmAmTNHQTGKSTELNTSDLRFQTGLEENDFNKNVLKR 234
                                     8        18     | |28   | |  38 |      48        58        68        78        88        98     | 108       118       128       138       148       158       168       178       188       198 |     208       218       228      
                                                    24-MSE  32 |     |                                                             104-MSE                                                                                       198-MSE                                
                                                      26-MSE  34     |                                                                                                                                                             200-MSE                              
                                                                    40-MSE
   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 3BK5)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BK5)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3BK5)

 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln A:60 - Pro A:61   [ 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 | 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
  3bk5
    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
  Q87Q63_VIBPA | Q87Q63
    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
  Q87Q63_VIBPA | Q87Q63
    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 3BK5)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3BK5)