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 :  CRYSTAL STRUCTURE OF THE DUAL-DOMAIN GGDEF-EAL MODULE OF FIMX FROM PSEUDOMONAS AERUGINOSA
 
Authors :  M. V. Navarro, N. De, N. Bae, Q. Wang, H. Sondermann
Date :  06 Feb 13  (Deposition) - 20 Feb 13  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Eal Phosphodiesterase, Hydrolase, Biofilm, C-Di-Gmp Effector, C-Di- Gmp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. V. Navarro, N. De, N. Bae, Q. Wang, H. Sondermann
Structural Analysis Of The Ggdef-Eal Domain-Containing C-Di-Gmp Receptor Fimx.
Structure V. 17 1104 2009
PubMed-ID: 19679088  |  Reference-DOI: 10.1016/J.STR.2009.06.010

(-) Compounds

Molecule 1 - FIMX
    Chains: A, B
    EC Number: 3.1.4.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPSUMO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: FIMX, PA4959
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4J40)

(-) Sites  (0, 0)

(no "Site" information available for 4J40)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J40)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:437 -Ala A:438
2Ala B:437 -Ala B:438

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J40)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J40)

(-) Exons   (0, 0)

(no "Exon" information available for 4J40)

(-) 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:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh.....eeeeee.ee......eeeeeeeeee.....eehhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhh.hhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhh....eeee.hhhhh...hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh..ee................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j40 A 437 AAQRGDVIAILQQALETNSFRLLFQPVISLRGDSHENYEVLLRLLNPQGQEVPPAEFLHAAKEAGLAEKIDRWVILNSIKLLAEHRAKGHQTKLFVHLSSASLQDPGLLPWLGVALKAARLPPESLVFQISEADATSYLKQAKQLTQGLATLHCQAAISQFGCSLNPFNALKHLTVQFIKIDGSFVQDLNQVENQEILKGLIAELHEQQKLSIVPFVESASVLATLWQAGATYIQGYYLQGPSQAMDYDFS 687
                                   446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686 


Chain B from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..eeeeeeeee......eeeeeeeeee.....eehhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhh.hhhhhhh............eeeeeehhhhhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhh....eeee.hhhhh...hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh..ee................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j40 B 437 AAQRGDVIAILQQALETNSFRLLFQPVISLRGDSHENYEVLLRLLNPQGQEVPPAEFLHAAKEAGLAEKIDRWVILNSIKLLAEHRAKGHQTKLFVHLSSASLQDPGLLPWLGVALKAARLPPESLVFQISEADATSYLKQAKQLTQGLATLHCQAAISQFGCSLNPFNALKHLTVQFIKIDGSFVQDLNQVENQEILKGLIAELHEQQKLSIVPFVESASVLATLWQAGATYIQGYYLQGPSQAMDYDFS 687
                                   446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686
   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 4J40)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J40)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J40)

(-) Gene Ontology  (4, 4)

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 4j40)
 
  Sites
(no "Sites" information available for 4j40)
 
  Cis Peptide Bonds
    Ala A:437 - Ala A:438   [ RasMol ]  
    Ala B:437 - Ala B:438   [ 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
  4j40
    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
  Q9HUK6_PSEAE | Q9HUK6
    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)
  3.1.4.52
    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
  Q9HUK6_PSEAE | Q9HUK6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9HUK6_PSEAE | Q9HUK6: 3hv8 3hv9 3hva 4afy 4ag0

(-) Related Entries Specified in the PDB File

3hv8 3hv9 3hva