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 A PUTATIVE METAL-DEPENDENT PHOSPHOESTERASE (BAD_1165) FROM BIFIDOBACTERIUM ADOLESCENTIS ATCC 15703 AT 2.40 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  31 Jul 08  (Deposition) - 02 Sep 08  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. W. Han, J. Ko, C. L. Farr, M. C. Deller, Q. Xu, H. J. Chiu, M. D. Miller, J. Sefcikova, S. Somarowthu, P. J. Beuning, M. A. Elsliger, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson, M. J. Ondrechen
Crystal Structure Of A Metal-Dependent Phosphoesterase (Yp_910028. 1) From Bifidobacterium Adolescentis: Computational Prediction And Experimental Validation Of Phosphoesterase Activity.
Proteins V. 79 2146 2011
PubMed-ID: 21538547  |  Reference-DOI: 10.1002/PROT.23035

(-) Compounds

Molecule 1 - PUTATIVE METAL-DEPENDENT PHOSPHOESTERASE
    Atcc: 15703
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_910028.1, BAD_1165
    Organism Scientific: BIFIDOBACTERIUM ADOLESCENTIS ATCC 15703
    Organism Taxid: 367928

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2FE2Ligand/IonFE (III) ION
3MSE4Mod. Amino AcidSELENOMETHIONINE
4PO42Ligand/IonPHOSPHATE ION
5ZN1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:24 , HIS A:49 , HIS A:262BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREGLU A:74 , HIS A:85 , HIS A:202BINDING SITE FOR RESIDUE FE A 302
3AC3SOFTWAREHIS A:17 , HIS A:19 , GLU A:74 , ASP A:260BINDING SITE FOR RESIDUE FE A 303
4AC4SOFTWAREHIS A:19 , ASP A:24 , HIS A:49 , GLU A:74 , HIS A:85 , ASP A:260 , HIS A:262 , LYS A:266 , HOH A:346BINDING SITE FOR RESIDUE PO4 A 304
5AC5SOFTWAREARG A:109 , ARG A:112 , ARG A:145 , HOH A:348 , HOH A:367 , HOH A:368BINDING SITE FOR RESIDUE PO4 A 305
6AC6SOFTWAREHIS A:185 , ASP A:224 , GLU A:239 , HOH A:355 , HOH A:363BINDING SITE FOR RESIDUE ACT A 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E0F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3E0F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E0F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E0F)

(-) Exons   (0, 0)

(no "Exon" information available for 3E0F)

(-) 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:286
 aligned with A1A2L3_BIFAA | A1A2L3 from UniProtKB/TrEMBL  Length:300

    Alignment length:286
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287      
         A1A2L3_BIFAA     8 EPPAQGWDIHCHTVFSDGTETPRTLVEQARKLGLHGVAIADHDTTAGWDEATEASEEIGLPLLLGTEITAVDEDVSVHMLAFQYDPSNEHISSMFANTRAARLRRTKRMVERLSQDFPITWDDVLAQVKEGERTTIGRPHIADALVAAGVYETRSDAFADAVSAKSKYYIPTPSPSTHEVIAAVKGAGGVVVAAHAGDPQRNRRLLSDEQLDAMIADGLDGLEVWHRGNPPEQRERLLTIAARHDLLVTGGSDWHGKGKPNGLGENLTDDDTVREILCRGVDLIGR 293
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.........hhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh...hhhhh..hhhhhhhhhhhh....hhhhhhh................hhhhhhhhhhhh..eeeee............hhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.eeee....hhhhh.........hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e0f A   8 EPPAQGWDIHCHTVFSDGTETPRTLVEQARKLGLHGVAIADHDTTAGWDEATEASEEIGLPLLLGTEITAVDEDVSVHmLAFQYDPSNEHISSmFANTRAARLRRTKRmVERLSQDFPITWDDVLAQVKEGERTTIGRPHIADALVAAGVYETRSDAFADAVSAKSKYYIPTPSPSTHEVIAAVKGAGGVVVAAHAGDPQRNRRLLSDEQLDAmIADGLDGLEVWHRGNPPEQRERLLTIAARHDLLVTGGSDWHGKGKPNGLGENLTDDDTVREILCRGVDLIGR 293
                                    17        27        37        47        57        67        77        87        97   |   107       117       127       137       147       157       167       177       187       197       207       217   |   227       237       247       257       267       277       287      
                                                                                                         86-MSE        101-MSE        116-MSE                                                                                                  221-MSE
   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 3E0F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E0F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E0F)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A1A2L3_BIFAA | A1A2L3)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    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: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.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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
(no "Cis Peptide Bonds" information available for 3e0f)
 

(-) 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
  3e0f
    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
  A1A2L3_BIFAA | A1A2L3
    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
  A1A2L3_BIFAA | A1A2L3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A1A2L3_BIFAA | A1A2L3: 3o0f

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3E0F)