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 LUXP FROM VIBRIO HARVEYI COMPLEXED WITH AUTOINDUCER-2
 
Authors :  X. Chen, S. Schauder, N. Potier, A. Van Dorsselaer, I. Pelczer, B. L. Bassler, F. M. Hughson
Date :  05 Sep 01  (Deposition) - 04 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Ligand Complex, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Chen, S. Schauder, N. Potier, A. Van Dorsselaer, I. Pelczer, B. L. Bassler, F. M. Hughson
Structural Identification Of A Bacterial Quorum-Sensing Signal Containing Boron.
Nature V. 415 545 2002
PubMed-ID: 11823863  |  Reference-DOI: 10.1038/415545A
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LUXP PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PGEX4T
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: LUXP
    Organism Scientific: VIBRIO HARVEYI
    Organism Taxid: 669

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1AI21Ligand/Ion3A-METHYL-5,6-DIHYDRO-FURO[2,3-D][1,3,2]DIOXABOROLE-2,2,6,6A-TETRAOL
2CA1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:149 , HOH A:677 , HOH A:684BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREGLN A:77 , SER A:79 , TYR A:81 , TRP A:82 , ASN A:159 , ARG A:215 , SER A:265 , THR A:266 , TRP A:289 , ARG A:310 , HOH A:417 , HOH A:479BINDING SITE FOR RESIDUE AI2 A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JX6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JX6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JX6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JX6)

(-) Exons   (0, 0)

(no "Exon" information available for 1JX6)

(-) 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:338
 aligned with LUXP_VIBHA | P54300 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:338
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356        
           LUXP_VIBHA    27 GYWGYQEFLDEFPEQRNLTNALSEAVRAQPVPLSKPTQRPIKISVVYPGQQVSDYWVRNIASFEKRLYKLNINYQLNQVFTRPNADIKQQSLSLMEALKSKSDYLIFTLDTTRHRKFVEHVLDSTNTKLILQNITTPVREWDKHQPFLYVGFDHAEGSRELATEFGKFFPKHTYYSVLYFSEGYISDVRGDTFIHQVNRDNNFELQSAYYTKATKQSGYDAAKASLAKHPDVDFIYACSTDVALGAVDALAELGREDIMINGWGGGSAELDAIQKGDLDITVMRMNDDTGIAMAEAIKWDLEDKPVPTVYSGDFEIVTKADSPERIEALKKRAFRYSD 364
               SCOP domains d1jx6a_ A: Quorum-sensing signal (autoinducer-2) binding protein LuxP                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1jx6A01 A:27-177,A:311-337,A:360-363  [code=3.40.50.2300, no name defined]                                                                             --1jx6A02 A:180-310,A:340-359  [code=3.40.50.2300, no name defined]                                                                  1jx6A01                    --1jx6A02             1jx6- CATH domains
               Pfam domains ------------------------------------------Peripla_BP_4-1jx6A01 A:69-330                                                                                                                                                                                                                                         ---------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeee......hhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhh..eeeee.....hhhhh.....eeee.hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh....ee.....hhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhh......eee..eeeee...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jx6 A  27 GYWGYQEFLDEFPEQRNLTNALSEAVRAQPVPLSKPTQRPIKISVVYPGQQVSDYWVRNIASFEKRLYKLNINYQLNQVFTRPNADIKQQSLSLMEALKSKSDYLIFTLDTTRHRKFVEHVLDSTNTKLILQNITTPVREWDKHQPFLYVGFDHAEGSRELATEFGKFFPKHTYYSVLYFSEGYISDVRGDTFIHQVNRDNNFELQSAYYTKATKQSGYDAAKASLAKHPDVDFIYACSTDVALGAVDALAELGREDIMINGWGGGSAELDAIQKGDLDITVMRMNDDTGIAMAEAIKWDLEDKPVPTVYSGDFEIVTKADSPERIEALKKRAFRYSD 364
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Periplas_BP (97)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LUXP_VIBHA | P54300)
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).
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 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
    AI2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1jx6)
 

(-) 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
  1jx6
    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
  LUXP_VIBHA | P54300
    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
  LUXP_VIBHA | P54300
    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
        LUXP_VIBHA | P54300: 1zhh 2hj9 4yp9 4yr7 4yrz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1JX6)