Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  MALONATE-BOUND STRUCTURE OF THE GLYCEROPHOSPHODIESTERASE FROM ENTEROBACTER AEROGENES (GPDQ) AND CHARACTERIZATION OF THE NATIVE FE2+ METAL ION PREFERENCE
 
Authors :  C. J. Jackson, P. D. Carr, D. L. Ollis
Date :  07 May 08  (Deposition) - 07 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  B,C
Biol. Unit 1:  B,C  (3x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Malonate, Metalloenzyme, Iron, Phosphodiesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Jackson, K. S. Hadler, P. D. Carr, A. J. Oakley, S. Yip, G. Schenk, D. L. Ollis
Malonate-Bound Structure Of The Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) And Characterization Of The Native Fe2+ Metal-Ion Preference.
Acta Crystallogr. , Sect. F V. 64 681 2008
PubMed-ID: 18678932  |  Reference-DOI: 10.1107/S1744309108017600

(-) Compounds

Molecule 1 - PHOSPHOHYDROLASE
    Chains: B, C
    EC Number: 3.1.4.46
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCY76
    Expression System Strain: DH5A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GPDQ
    Organism Scientific: ENTEROBACTER AEROGENES
    Organism Taxid: 548
    Synonym: GPDQ, GLYCEROPHOSPHODIESTERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : BC
Biological Unit 1 (3x): BC
Biological Unit 2 (1x): BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1FE24Ligand/IonFE (II) ION
2MLI2Ligand/IonMALONATE ION
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1FE212Ligand/IonFE (II) ION
2MLI6Ligand/IonMALONATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1FE24Ligand/IonFE (II) ION
2MLI2Ligand/IonMALONATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:8 , HIS B:10 , ASP B:50 , HIS B:197BINDING SITE FOR RESIDUE FE2 B 275
2AC2SOFTWAREASP B:50 , ASN B:80 , HIS B:156 , HIS B:195BINDING SITE FOR RESIDUE FE2 B 276
3AC3SOFTWAREASP C:8 , HIS C:10 , ASP C:50 , HIS C:197BINDING SITE FOR RESIDUE FE2 C 275
4AC4SOFTWAREASP C:50 , ASN C:80 , HIS C:156 , HIS C:195BINDING SITE FOR RESIDUE FE2 C 276
5AC5SOFTWAREASP B:8 , HIS B:10 , ASP B:50 , ASN B:80 , HIS B:81 , HIS B:195 , HIS B:197BINDING SITE FOR RESIDUE MLI B 277
6AC6SOFTWAREASP C:8 , HIS C:10 , ASP C:50 , ASN C:80 , HIS C:81 , ILE C:170 , HIS C:195 , HIS C:197BINDING SITE FOR RESIDUE MLI C 277

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1B:54 -C:269
2B:269 -C:54

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly B:259 -Pro B:260
2Gly C:259 -Pro C:260

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZO9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZO9)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZO9)

(-) Sequences/Alignments

Asymmetric 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 B from PDB  Type:PROTEIN  Length:271
 aligned with Q6XBH1_ENTAE | Q6XBH1 from UniProtKB/TrEMBL  Length:274

    Alignment length:271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270 
         Q6XBH1_ENTAE     1 MLLAHISDTHFRSRGEKLYGFIDVNAANADVVSQLNALRERPDAVVVSGDIVNCGRPEEYQVARQILGSLNYPLYLIPGNHDDKALFLEYLQPLCPQLGSDANNMRCAVDDFATRLLFIDSSRAGTSKGWLTDETISWLEAQLFEGGDKPATIFMHHPPLPLGNAQMDPIACENGHRLLALVERFPSLTRIFCGHNHSLTMTQYRQALISTLPGTVHQVPYCHEDTRPYYDLSPASCLMHRQVGEQWVSYQHSLAHYAGPWLYDENISCPT 271
               SCOP domains d2zo9b1 B:1-271 Glycerophosphodiesterase GpdQ                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..........hhhhh.hhhhhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhh......eeee.....eeeee............hhhhhhhhhhhhhh.....eeeee...........hhhhh...hhhhhhhhhhh..eeeeee......eeeee..eeeee.................ee.....eeeeeeee..eeeeeeee.......ee.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zo9 B   1 MLLAHISDTHFRSRGEKLYGFIDVNAANADVVSQLNALRERPDAVVVSGDIVNCGRPEEYQVARQILGSLNYPLYLIPGNHDDKALFLEYLQPLCPQLGSDANNMRCAVDDFATRLLFIDSSRAGTSKGWLTDETISWLEAQLFEGGDKPATIFMHHPPLPLGNAQMDPIACENGHRLLALVERFPSLTRIFCGHNHSLTMTQYRQALISTLPGTVHQVPYCHADTDPYYDLSPASCLMHRQVGEQWVSYQHSLAHYAGPWLYDENISCPT 271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270 


Chain C from PDB  Type:PROTEIN  Length:271
 aligned with Q6XBH1_ENTAE | Q6XBH1 from UniProtKB/TrEMBL  Length:274

    Alignment length:271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270 
         Q6XBH1_ENTAE     1 MLLAHISDTHFRSRGEKLYGFIDVNAANADVVSQLNALRERPDAVVVSGDIVNCGRPEEYQVARQILGSLNYPLYLIPGNHDDKALFLEYLQPLCPQLGSDANNMRCAVDDFATRLLFIDSSRAGTSKGWLTDETISWLEAQLFEGGDKPATIFMHHPPLPLGNAQMDPIACENGHRLLALVERFPSLTRIFCGHNHSLTMTQYRQALISTLPGTVHQVPYCHEDTRPYYDLSPASCLMHRQVGEQWVSYQHSLAHYAGPWLYDENISCPT 271
               SCOP domains d2zo9c_ C: Glycerophosphodiesterase GpdQ                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Metallophos-2zo9C01 C:1-199                                                                                                                                                                            ------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) Metallophos-2zo9C02 C:1-199                                                                                                                                                                            ------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .eeeee..........hhhhh.hhhhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhh.....eeee.....hhhhhhhhhh..hhhhh.......eee.....eeee.............hhhhhhhhhhhhhhhh...eeeee...........hhhhh...hhhhhhhhhhh..eeeeee......eeeee..eeeee.................ee.....eeeeeeee..eeeeeeee.......ee.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zo9 C   1 MLLAHISDTHFRSRGEKLYGFIDVNAANADVVSQLNALRERPDAVVVSGDIVNCGRPEEYQVARQILGSLNYPLYLIPGNHDDKALFLEYLQPLCPQLGSDANNMRCAVDDFATRLLFIDSSRAGTSKGWLTDETISWLEAQLFEGGDKPATIFMHHPPLPLGNAQMDPIACENGHRLLALVERFPSLTRIFCGHNHSLTMTQYRQALISTLPGTVHQVPYCHADTDPYYDLSPASCLMHRQVGEQWVSYQHSLAHYAGPWLYDENISCPT 271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZO9)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Calcineurin (56)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain B,C   (Q6XBH1_ENTAE | Q6XBH1)
molecular function
    GO:0004115    3',5'-cyclic-AMP phosphodiesterase activity    Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.

 Visualization

(-) Interactive Views

Asymmetric 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
    FE2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLI  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly B:259 - Pro B:260   [ RasMol ]  
    Gly C:259 - Pro C:260   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  2zo9
    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
  Q6XBH1_ENTAE | Q6XBH1
    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)
  3.1.4.46
    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
  Q6XBH1_ENTAE | Q6XBH1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q6XBH1_ENTAE | Q6XBH1: 2dxl 2dxn 2zoa 3d03

(-) Related Entries Specified in the PDB File

2dxn GPDQ WITH BOUND ZINC
2zoa