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 :  1.55 A CRYSTAL STRUCTURE OF XANTHOMONAS CITRI FIMX EAL DOMAIN IN COMPLEX WITH C-DIGMP
 
Authors :  C. S. Farah, C. R. Guzzo
Date :  20 Jun 12  (Deposition) - 27 Mar 13  (Release) - 12 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim Like Barrel, Beta-(Beta/Alpha)6-Beta, C-Di-Gmp Binding, Type Iv Pilus Assembly, Pilz, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. R. Guzzo, G. Dunger, R. K. Salinas, C. S. Farah
Structure Of The Pilz-Fimxeal-C-Di-Gmp Complex Responsible For The Regulation Of Bacterial Type Iv Pilus Biogenesis.
J. Mol. Biol. V. 425 2174 2013
PubMed-ID: 23507310  |  Reference-DOI: 10.1016/J.JMB.2013.03.021

(-) Compounds

Molecule 1 - FIMX
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: EAL DOMAIN (UNP RESIDUES 426-689)
    Gene: XAC2398
    Organism Scientific: XANTHOMONAS AXONOPODIS PV. CITRI
    Organism Taxid: 190486
    Strain: 306

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1C2E1Ligand/Ion9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:463 , PHE A:479 , LEU A:480 , ARG A:481 , SER A:490 , PRO A:491 , ASN A:492 , MET A:495 , ASP A:508 , ARG A:534 , ARG A:550 , GLU A:551 , ALA A:554 , GLU A:653 , PHE A:654 , GLN A:673 , GLY A:674 , ASP A:675 , THR A:680 , HOH A:804 , HOH A:807 , HOH A:820 , HOH A:822 , HOH A:854 , HOH A:878 , HOH A:906 , HOH A:955 , HOH A:974 , HOH A:1000 , HOH A:1013 , HOH A:1073BINDING SITE FOR RESIDUE C2E A 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FOJ)

(-) 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:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh..eeeeeee.ee.....eeeeeeeeee..eee....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh.hhhhhhhhhhhhhhhh.hhh.eeeeeehhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhh...eeeehhhhhh....hhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhh...ee................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4foj A 435 DRAEEERIERWVEQLREALVGDGFLLHYQPVLNLQPLELYQAFLRLERNGEMMSPNAFMAIAEEHDLVTEIDRWVVARAIRQLGERQRAGHKTHLLVRIGPNSFSDPQMIDTIREQLAVYGVPGERLWLQTPESKVFTHLRNAQQFLAAVSAMDCKVGLEQFGSGLDSFQLLAHFHPAFLKLDRGITGDIASARDSQEKIREITSRAQPAGILTMAEFVADAQSMSSFFSAGVDYVQGDFVAPTGPLMNYEFG 689
                                   444       454       464    || 476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686   
                                                            469|                                                                                                                                                                                                                         
                                                             472
   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 4FOJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

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
    C2E  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4foj)
 

(-) 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
  4foj
    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
  Q8PJX9_XANAC | Q8PJX9
    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
  Q8PJX9_XANAC | Q8PJX9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8PJX9_XANAC | Q8PJX9: 4fok 4fou

(-) Related Entries Specified in the PDB File

3cnr XANTHOMONAS AXONOPODIS PV CITRI PILZ (XAC1133)
4fok 1.8 A CRYSTAL STRUCTURE OF THE FIMX EAL DOMAIN IN COMPLEX WITH C-DIGMP
4fou 2.1 A CRYSTAL STRUCTURE OF PILZ-FIMX(EAL DOMAIN) IN COMPLEX WITH C-DIGMP