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 CBS DOMAINS FROM THE BACILLUS SUBTILIS CCPN REPRESSOR COMPLEXED WITH ADP
 
Authors :  D. Chaix, S. Arold, F. Hoh, N. Declerck
Date :  19 Jan 09  (Deposition) - 26 Jan 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cbs Domain Dimer, Metabolism Regulator, Central Glycolytic Gene Regulator, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Chaix, K. De Guillen, D. L. Coq, F. Hoh, C. Roumestand, S. Aymerich, S. T. Arold, N. Declerck
Ligand Recognition By The Energy Sensor Domain Of The Ccpn Repressor
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - YQZB PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CBS DOMAIN, REGULATORY DOMAIN OF THE TRANSCRIPTION FACTOR CCPN, UNP RESIDUES 63-212
    Gene: YQZB
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168
    Synonym: CENTRAL GLYCOLYTIC GENE REGULATOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:125 , ARG A:126 , LYS A:127 , ASP A:128 , THR A:149 , ILE A:154 , THR A:155 , GLN A:174 , ILE A:175 , ASP A:176 , ALA A:177 , HOH A:228 , ARG B:126BINDING SITE FOR RESIDUE ADP A 221
2AC2SOFTWAREARG A:126 , VAL B:123 , SER B:125 , LYS B:127 , ASP B:128 , THR B:149 , ASN B:153 , ILE B:154 , THR B:155 , GLN B:174 , ILE B:175 , ASP B:176 , ALA B:177 , LEU B:178 , HOH B:229BINDING SITE FOR RESIDUE ADP B 221

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Met A:151 -Pro A:152
2Met B:151 -Pro B:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBSPS51371 CBS domain profile.CCPN_BACSU83-139
 
148-211
 		  4A:83-139
B:83-139
A:148-211
B:148-209

(-) Exons   (0, 0)

(no "Exon" information available for 3FWR)

(-) 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:145
 aligned with CCPN_BACSU | O34994 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:145
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207     
           CCPN_BACSU    68 TQLLADKLKKLQVKDFQSIPVVIHENVSVYDAICTMFLEDVGTLFVVDRDAVLVGVLSRKDLLRASIGQQELTSVPVHIIMTRMPNITVCRREDYVMDIAKHLIEKQIDALPVIKDTDKGFEVIGRVTKTNMTKILVSLSENEIL 212
               SCOP domains d3fwra_ A: automated matches                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.....eee...hhhhhhhhhhhh...eeeee.....eeeeeehhhhhhhhhhh......hhhhh.ee......ee...hhhhhhhhhhhh...eeeeeee....eeeeeeeehhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------CBS  PDB: A:83-139 UniProt: 83-139                       --------CBS  PDB: A:148-211 UniProt: 148-211                            - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fwr A  68 TQLLADKLKKLQVKDFQSIPVVIHENVSVYDAICTMFLEDVGTLFVVDRDAVLVGVLSRKDLLRASIGQQELTSVPVHIIMTRMPNITVCRREDYVMDIAKHLIEKQIDALPVIKDTDKGFEVIGRVTKTNMTKILVSLSENEIL 212
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207     


Chain B from PDB  Type:PROTEIN  Length:146
 aligned with CCPN_BACSU | O34994 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:146
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203      
           CCPN_BACSU    64 GKTGTQLLADKLKKLQVKDFQSIPVVIHENVSVYDAICTMFLEDVGTLFVVDRDAVLVGVLSRKDLLRASIGQQELTSVPVHIIMTRMPNITVCRREDYVMDIAKHLIEKQIDALPVIKDTDKGFEVIGRVTKTNMTKILVSLSEN 209
               SCOP domains d3fwrb_ B: automated matches                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.....eee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh.......hhhhhhee...........hhhhhhhhhhhhh..eeeeeeee..eeeeeeeeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------CBS  PDB: B:83-139 UniProt: 83-139                       --------CBS  PDB: B:148-209 UniProt: 148-211                           PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fwr B  64 GKTGTQLLADKLKKLQVKDFQSIPVVIHENVSVYDAICTMFLEDVGTLFVVDRDAVLVGVLSRKDLLRASIGQQELTSVPVHIIMTRMPNITVCRREDYVMDIAKHLIEKQIDALPVIKDTDKGFEVIGRVTKTNMTKILVSLSEN 209
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FWR)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CCPN_BACSU | O34994)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0045013    carbon catabolite repression of transcription    A transcription regulation process in which the presence of one carbon source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources. Carbon catabolite repression is a mechanism of genetic regulation which the accumulation of catabolites of one substance in the cell represses the formation of enzymes that contribute to the catabolism of other substances.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Met A:151 - Pro A:152   [ RasMol ]  
    Met B:151 - Pro B:152   [ 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
  3fwr
    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
  CCPN_BACSU | O34994
    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
  CCPN_BACSU | O34994
    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
        CCPN_BACSU | O34994: 3fv6 3fws

(-) Related Entries Specified in the PDB File

3fv6 THE SAME PROTEIN
3fws THE SAME PROTEIN COMPLEXED WITH APPNP, PHOSPHATE AND MAGNESIUM IONS