Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE BIOTIN CARBOXYLASE DOMAIN OF PYRUVATE CARBOXYLASE
 
Authors :  S. Kondo, Y. Nakajima, S. Sugio, S. Sueda, M. N. Islam, H. Kondo
Date :  27 Sep 06  (Deposition) - 25 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Biotin Carboxylase, Pyruvate Carboxylase, Bacillus Thermodenitrificans, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Kondo, Y. Nakajima, S. Sugio, S. Sueda, M. N. Islam, H. Kondo
Structure Of The Biotin Carboxylase Domain Of Pyruvate Carboxylase From Bacillus Thermodenitrificans
Acta Crystallogr. , Sect. D V. 63 885 2007
PubMed-ID: 17642515  |  Reference-DOI: 10.1107/S0907444907029423
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRUVATE CARBOXYLASE
    ChainsA, B
    EC Number6.4.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTRC99A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentBIOTIN CARBOXYLASE DOMAIN
    Organism ScientificGEOBACILLUS THERMODENITRIFICANS
    Organism Taxid33940

 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 2DZD)

(-) Sites  (0, 0)

(no "Site" information available for 2DZD)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DZD)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:158 -Pro A:159
2Ala A:247 -Pro A:248
3Tyr B:158 -Pro B:159
4Ala B:247 -Pro B:248

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DZD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DZD)

(-) Exons   (0, 0)

(no "Exon" information available for 2DZD)

(-) 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:459
 aligned with Q05FZ3_GEOTD | Q05FZ3 from UniProtKB/TrEMBL  Length:461

    Alignment length:459
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452         
         Q05FZ3_GEOTD     3 TRRIRKVLVANRGEIAIRVFRACTELGIRTVAIYSKEDVGSYHRYKADEAYLVGEGKKPIEAYLDIEGIIEIAKAHDVDAIHPGYGFLSENIQFAKRCREEGIIFIGPNENHLDMFGDKVKARHAAVNAGIPVIPGSDGPVDGLEDVVAFAEAHGYPIIIKAALGGGGRGMRIVRSKSEVKEAFERAKSEAKAAFGSDEVYVEKLIENPKHIEVQILGDYEGNIVHLYERDCSVQRRHQKVVEVAPSVSLSDELRQRICEAAVQLMRSVGYVNAGTVEFLVSGDEFYFIEVNPRIQVEHTITEMITGIDIVQSQILIADGCSLHSHEVGIPKQEDIRINGYAIQSRVTTEDPLNNFMPDTGKIMAYRSGGGFGVRLDAGNGFQGAVITPYYDSLLVKLSTWALTFEQAARKMLRNLREFRIRGIKTNIPFLENVVQHPKFLSGEYDTSFIDTTPELFVF 461
               SCOP domains d2dzda1 A:3-120 automated matches                                                                                     d2dzda2 A:121-339 automated matches                                                                                                                                                                                        d2dzda3 A:340-461 automated matches                                                                                        SCOP domains
               CATH domains 2dzdA01 A:3-135  [code=3.40.50.20, no name defined]                                                                                  2dzdA02 A:136-207 ATP-grasp fold, A domain                              2dzdA03 A:208-461 ATP-grasp fold, B domain                                                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhhhhhh.eeeeeehhhhh..hhhhhh..eee.......hhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhh..ee...hhhhhhhh.hhhhhhhhhhhh.............hhhhhhhhhhhhh..eeeee........eeee.hhhhhhhhhhhhhhhhhhhh....eeeee.....eeeeeeeee.....eeeeeeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeee...hhhhhhhhhhhh.hhhhhhhhhhh............hhhhh....eeeeeeee..hhhhh.....ee..eee......eeeee.......ee......eeeeeeeee.hhhhhhhhhhhhhhh.eee....hhhhhhhhhhhhhhhh.....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dzd A   3 TRRIRKVLVANRGEIAIRVFRACTELGIRTVAIYSKEDVGSYHRYKADEAYLVGEGKKPIEAYLDIEGIIEIAKAHDVDAIHPGYGFLSENIQFAKRCREEGIIFIGPNENHLDMFGDKVKARHAAVNAGIPVIPGSDGPVDGLEDVVAFAEAHGYPIIIKAALGGGGRGMRIVRSKSEVKEAFERAKSEAKAAFGSDEVYVEKLIENPKHIEVQILGDYEGNIVHLYERDCSVQRRHQKVVEVAPSVSLSDELRQRICEAAVQLMRSVGYVNAGTVEFLVSGDEFYFIEVNPRIQVEHTITEMITGIDIVQSQILIADGCSLHSHEVGIPKQEDIRINGYAIQSRVTTEDPLNNFMPDTGKIMAYRSGGGFGVRLDAGNGFQGAVITPYYDSLLVKLSTWALTFEQAARKMLRNLREFRIRGIKTNIPFLENVVQHPKFLSGEYDTSFIDTTPELFVF 461
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452         

Chain B from PDB  Type:PROTEIN  Length:453
 aligned with Q05FZ3_GEOTD | Q05FZ3 from UniProtKB/TrEMBL  Length:461

    Alignment length:459
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452         
         Q05FZ3_GEOTD     3 TRRIRKVLVANRGEIAIRVFRACTELGIRTVAIYSKEDVGSYHRYKADEAYLVGEGKKPIEAYLDIEGIIEIAKAHDVDAIHPGYGFLSENIQFAKRCREEGIIFIGPNENHLDMFGDKVKARHAAVNAGIPVIPGSDGPVDGLEDVVAFAEAHGYPIIIKAALGGGGRGMRIVRSKSEVKEAFERAKSEAKAAFGSDEVYVEKLIENPKHIEVQILGDYEGNIVHLYERDCSVQRRHQKVVEVAPSVSLSDELRQRICEAAVQLMRSVGYVNAGTVEFLVSGDEFYFIEVNPRIQVEHTITEMITGIDIVQSQILIADGCSLHSHEVGIPKQEDIRINGYAIQSRVTTEDPLNNFMPDTGKIMAYRSGGGFGVRLDAGNGFQGAVITPYYDSLLVKLSTWALTFEQAARKMLRNLREFRIRGIKTNIPFLENVVQHPKFLSGEYDTSFIDTTPELFVF 461
               SCOP domains d2dzdb1 B:3-120 automated matches                                                                                     d2dzdb2 B:121-339 automated matches                                                                                                                                                                                        d2dzdb3 B:340-461 automated matches                                                                                        SCOP domains
               CATH domains 2dzdB01 B:3-135  [code=3.40.50.20, no name defined]                                                                                  2dzdB02 B:136-207 ATP-grasp fold, A domain                              2dzdB03 B:208-461 ATP-grasp fold, B domain                                                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhh.eeee.....hhhhhh.hhhhhhhhhhhh...eee........hhhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhh..eeeee........eeee.hhhhhhhhhhhhhhhhh------.eeeee.....eeeeeeeee.....eeeeeeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..eeeeeeee.....hhhhhhhhhh.hhhhhhhhhhh.....................eeeeeeee............ee..eee......eeeee.......ee......eeeeeeeee.hhhhhhhhhhhhhhhheee....hhhhhhhhhhhhhhhh......hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dzd B   3 TRRIRKVLVANRGEIAIRVFRACTELGIRTVAIYSKEDVGSYHRYKADEAYLVGEGKKPIEAYLDIEGIIEIAKAHDVDAIHPGYGFLSENIQFAKRCREEGIIFIGPNENHLDMFGDKVKARHAAVNAGIPVIPGSDGPVDGLEDVVAFAEAHGYPIIIKAALGGGGRGMRIVRSKSEVKEAFERAKSEAK------EVYVEKLIENPKHIEVQILGDYEGNIVHLYERDCSVQRRHQKVVEVAPSVSLSDELRQRICEAAVQLMRSVGYVNAGTVEFLVSGDEFYFIEVNPRIQVEHTITEMITGIDIVQSQILIADGCSLHSHEVGIPKQEDIRINGYAIQSRVTTEDPLNNFMPDTGKIMAYRSGGGFGVRLDAGNGFQGAVITPYYDSLLVKLSTWALTFEQAARKMLRNLREFRIRGIKTNIPFLENVVQHPKFLSGEYDTSFIDTTPELFVF 461
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192 |     202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452         
                                                                                                                                                                                                                         194    201                                                                                                                                                                                                                                                                    

   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  (3, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DZD)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q05FZ3_GEOTD | Q05FZ3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004075    biotin carboxylase activity    Catalysis of the reaction: ATP + biotin-carboxyl-carrier protein + CO2 = ADP + phosphate + carboxybiotin-carboxyl-carrier protein.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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 2dzd)
 
  Sites
(no "Sites" information available for 2dzd)
 
  Cis Peptide Bonds
    Ala A:247 - Pro A:248   [ RasMol ]  
    Ala B:247 - Pro B:248   [ RasMol ]  
    Tyr A:158 - Pro A:159   [ RasMol ]  
    Tyr B:158 - Pro B:159   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2dzd
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q05FZ3_GEOTD | Q05FZ3
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  6.4.1.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q05FZ3_GEOTD | Q05FZ3
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2DZD)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2DZD)