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 THE FIMX EAL DOMAIN IN COMPLEX WITH REACTION PRODUCT PGPG
 
Authors :  J. Robert-Paganin, S. Nonin-Lecomte, S. Rety
Date :  23 Jan 12  (Deposition) - 09 Jan 13  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase, Cdigmp Biofilm, Phosphodiesterase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Robert-Paganin, S. Nonin-Lecomte, S. Rety
Crystal Structure Of An Eal Domain In Complex With Reaction Product 5'-Pgpg
Plos One V. 7 52424 2012
PubMed-ID: 23285035  |  Reference-DOI: 10.1371/JOURNAL.PONE.0052424

(-) Compounds

Molecule 1 - FIMX
    Chains: A, B
    EC Number: 3.1.4.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: ROSETTA 2
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Fragment: EAL DOMAIN, RESIDUES 439-691
    Gene: PA4959
    Organism Scientific: PSEUDOMONAS AERUGINOSA PAO1
    Organism Taxid: 208964
 
Molecule 2 - 5'-R(*GP*GP)-3'
    Chains: C, D
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2NA2Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:461 , GLU A:475 , GLN A:671 , HOH A:2134 , G C:1 , G C:2BINDING SITE FOR RESIDUE MG A 801
2AC2SOFTWAREASP A:442 , HOH A:2010 , HOH A:2135BINDING SITE FOR RESIDUE MG A 802
3AC3SOFTWARETHR A:582 , ALA A:592 , THR A:611 , HOH A:2072BINDING SITE FOR RESIDUE NA A 803
4AC4SOFTWARELYS A:635 , THR A:661 , GLN A:664 , ALA A:665 , HOH B:2117BINDING SITE FOR RESIDUE NA A 804
5AC5SOFTWAREGLN B:461 , GLU B:475 , GLN B:671 , HOH B:2125 , G D:1 , G D:2BINDING SITE FOR RESIDUE MG B 801

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AFY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4AFY)

(-) 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:250
 aligned with Q9HUK6_PSEAE | Q9HUK6 from UniProtKB/TrEMBL  Length:691

    Alignment length:250
                                   447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687
         Q9HUK6_PSEAE   438 AQRGDVIAILQQALETNSFRLLFQPVISLRGDSHENYEVLLRLLNPQGQEVPPAEFLHAAKEAGLAEKIDRWVILNSIKLLAEHRAKGHQTKLFVHLSSASLQDPGLLPWLGVALKAARLPPESLVFQISEADATSYLKQAKQLTQGLATLHCQAAISQFGCSLNPFNALKHLTVQFIKIDGSFVQDLNQVENQEILKGLIAELHEQQKLSIVPFVESASVLATLWQAGATYIQGYYLQGPSQAMDYDFS 687
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh..eeeeeeeee......eeeeeeee.........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhh..hhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhh..eeeeeee......hhhhh.....eeee.hhhhh...hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh..ee................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4afy A 438 MQRGDVIAILQQALETNSFRLLFQPVISLRGDSHENYEVLLRLLNPQGQEVPPAEFLHAAKEAGLAEKIDRWVILNSIKLLAEHRAKGHQTKLFVHLSSASLQDPGLLPWLGVALKAARLPPESLVFQISEADATSYLKQAKQLTQGLATLHCQAAISQFGCSLNPFNALKHLTVQFIKIDGSFVQDLNQVENQEILKGLIAELHEQQKLSIVPFVESASVLATLWQAGATYIQGYYLQGPSQAMDYDFS 687
                                   447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687


Chain B from PDB  Type:PROTEIN  Length:251
 aligned with Q9HUK6_PSEAE | Q9HUK6 from UniProtKB/TrEMBL  Length:691

    Alignment length:251
                                   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 
         Q9HUK6_PSEAE   437 AAQRGDVIAILQQALETNSFRLLFQPVISLRGDSHENYEVLLRLLNPQGQEVPPAEFLHAAKEAGLAEKIDRWVILNSIKLLAEHRAKGHQTKLFVHLSSASLQDPGLLPWLGVALKAARLPPESLVFQISEADATSYLKQAKQLTQGLATLHCQAAISQFGCSLNPFNALKHLTVQFIKIDGSFVQDLNQVENQEILKGLIAELHEQQKLSIVPFVESASVLATLWQAGATYIQGYYLQGPSQAMDYDFS 687
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh.eeeeeee.ee......eeeeeeeeee.....eehhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhh.hhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhh....eeee.hhhhh...hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...ee................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4afy B 437 HMQRGDVIAILQQALETNSFRLLFQPVISLRGDSHENYEVLLRLLNPQGQEVPPAEFLHAAKEAGLAEKIDRWVILNSIKLLAEHRAKGHQTKLFVHLSSASLQDPGLLPWLGVALKAARLPPESLVFQISEADATSYLKQAKQLTQGLATLHCQAAISQFGCSLNPFNALKHLTVQFIKIDGSFVQDLNQVENQEILKGLIAELHEQQKLSIVPFVESASVLATLWQAGATYIQGYYLQGPSQAMDYDFS 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 C from PDB  Type:RNA  Length:2
                                  
                 4afy C   1 GG   2


Chain D from PDB  Type:RNA  Length:2
                                  
                 4afy D   1 GG   2
   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 4AFY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9HUK6_PSEAE | Q9HUK6)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

 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 ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4afy)
 

(-) 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
  4afy
    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 4ag0 4j40

(-) Related Entries Specified in the PDB File

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