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 :  STRUCTURAL CHARACTERIZATION OF THE PPX/GPPA PROTEIN FAMILY: CRYSTAL STRUCTURE OF THE AQUIFEX AEOLICUS FAMILY MEMBER
 
Authors :  O. Kristensen, M. Laurberg, A. Liljas, J. S. Kastrup, M. Gajhede
Date :  06 May 04  (Deposition) - 03 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta Protein, Actin-Like Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Kristensen, M. Laurberg, A. Liljas, J. S. Kastrup, M. Gajhede
Structural Characterization Of The Stringent Response Related Exopolyphosphatase/Guanosine Pentaphosphate Phosphohydrolase Protein Family
Biochemistry V. 43 8894 2004
PubMed-ID: 15248747  |  Reference-DOI: 10.1021/BI049083C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EXOPOLYPHOSPHATASE
    Chains: A
    EC Number: 3.6.1.11, 3.6.1.40
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PPX
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: PPX/GPPA PHOSPHATASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL3Ligand/IonCHLORIDE ION
3IOD1Ligand/IonIODIDE ION
4MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:226BINDING SITE FOR RESIDUE IOD A 501
02AC2SOFTWAREASP A:141 , GLY A:143 , SER A:146 , GLU A:148 , HOH A:685 , HOH A:689BINDING SITE FOR RESIDUE CA A 502
03AC3SOFTWAREGLN A:142 , GLY A:143 , GLY A:145 , GLY A:166 , ILE A:167BINDING SITE FOR RESIDUE CL A 503
04AC4SOFTWAREGLY A:166 , ASN A:169 , HOH A:624 , HOH A:972BINDING SITE FOR RESIDUE CL A 504
05AC5SOFTWAREGLN A:142 , ARG A:267BINDING SITE FOR RESIDUE CL A 505
06AC6SOFTWARELYS A:78 , LYS A:258 , HOH A:803 , HOH A:975BINDING SITE FOR RESIDUE MPD A 600
07AC7SOFTWAREHIS A:232 , HOH A:976BINDING SITE FOR RESIDUE MPD A 601
08AC8SOFTWAREGLU A:80 , ARG A:81 , VAL A:82 , ARG A:259 , MPD A:603 , HOH A:695BINDING SITE FOR RESIDUE MPD A 602
09AC9SOFTWAREARG A:81 , TRP A:244 , THR A:247 , GLU A:309 , MPD A:602 , HOH A:966BINDING SITE FOR RESIDUE MPD A 603
10BC1SOFTWAREGLU A:136 , LYS A:153 , ARG A:158 , TYR A:238 , GLU A:283 , HOH A:649 , HOH A:753 , HOH A:759BINDING SITE FOR RESIDUE MPD A 604
11BC2SOFTWAREGLN A:118 , TYR A:122 , LEU A:125 , SER A:304BINDING SITE FOR RESIDUE MPD A 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T6C)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:178 -Pro A:179
2Tyr A:224 -Pro A:225

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T6C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T6C)

(-) Exons   (0, 0)

(no "Exon" information available for 1T6C)

(-) 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:306
 aligned with O67040_AQUAE | O67040 from UniProtKB/TrEMBL  Length:312

    Alignment length:306
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306      
         O67040_AQUAE     7 PIMRVASIDIGSYSVRLTIAQIKDGKLSIILERGRITSLGTKVKETGRLQEDRIEETIQVLKEYKKLIDEFKVERVKAVATEAIRRAKNAEEFLERVKREVGLVVEVITPEQEGRYAYLAVAYSLKPEGEVCVVDQGGGSTEYVFGKGYKVREVISLPIGIVNLTETFFKQDPPTEEEVKRFFEFLEKELSKVKKPVDTIVGLGGTITTLAALEYNVYPYDPQKVHGKVLTYGQIKKWFDTFKEIPSEERSKRFRQVEDRRAKVILAGIGIFLKTLEIFEKDCLIVSDWGLREGVLVSEVLKENHS 312
               SCOP domains d1t6ca1 A:7-132 Exopolyphosphatase Ppx                                                                                        d1t6ca2 A:133-312 Exopolyphosphatase Ppx                                                                                                                                             SCOP domains
               CATH domains 1t6cA01 A:7-131  [code=3.30.420.40, no name defined]                                                                         1t6cA02 A:132-312 Exopolyphosphatase. Domain 2                                                                                                                                        CATH domains
               Pfam domains -----------------Ppx-GppA-1t6cA01 A:24-309                                                                                                                                                                                                                                                                     --- Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeeeee..eeeeeeeeeee.....hhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhh..hhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeee..eeeeeeee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhh.....hhhhhh..eeehhhhhhhhhhhh..hhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t6c A   7 PIMRVASIDIGSYSVRLTIAQIKDGKLSIILERGRITSLGTKVKETGRLQEDRIEETIQVLKEYKKLIDEFKVERVKAVATEAIRRAKNAEEFLERVKREVGLVVEVITPEQEGRYAYLAVAYSLKPEGEVCVVDQGGGSTEYVFGKGYKVREVISLPIGIVNLTETFFKQDPPTEEEVKRFFEFLEKELSKVKKPVDTIVGLGGTITTLAALEYNVYPYDPQKVHGKVLTYGQIKKWFDTFKEIPSEERSKRFRQVEDRRAKVILAGIGIFLKTLEIFEKDCLIVSDWGLREGVLVSEVLKENHS 312
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306
   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) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Actin_ATPase (173)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O67040_AQUAE | O67040)
molecular function
    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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IOD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:178 - Pro A:179   [ RasMol ]  
    Tyr A:224 - Pro A:225   [ 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
  1t6c
    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
  O67040_AQUAE | O67040
    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)
  3.6.1.11
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  3.6.1.40
    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
  O67040_AQUAE | O67040
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O67040_AQUAE | O67040: 1t6d 2j4r

(-) Related Entries Specified in the PDB File

1t6d THE SAME PROTEIN(V82M/C138M/V306M) AT RESOLUTION 2.15 A