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 :  X-RAY CRYSTALLOGRAPHIC STRUCTURES SHOW CONSERVATION OF A TRIGONAL-BIPYRAMIDAL INTERMEDIATE IN A PHOSPHORYL-TRANSFER SUPERFAMILY.
 
Authors :  Z. Lu, D. Dunaway-Mariano, K. N. Allen
Date :  19 Sep 07  (Deposition) - 22 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Had-Like Phosphatase, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Lu, D. Dunaway-Mariano, K. N. Allen
The Catalytic Scaffold Of The Haloalkanoic Acid Dehalogenas Enzyme Superfamily Acts As A Mold For The Trigonal Bipyramidal Transition State.
Proc. Natl. Acad. Sci. Usa V. 105 5687 2008
PubMed-ID: 18398008  |  Reference-DOI: 10.1073/PNAS.0710800105

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3A-HPP
    Expression System Strain: BL21DE3PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BACTEROIDES THETAIOTAOMICRON
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 226186
    Strain: VPI-5482

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2VN41Ligand/IonOXIDO(DIOXO)VANADIUM

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , ASP A:10 , ASP A:211 , HOH A:603 , HOH A:605BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREASP A:8 , ILE A:9 , ASP A:10 , THR A:43 , GLY A:44 , TRP A:174 , LYS A:188 , ASN A:214 , HOH A:603 , HOH A:686BINDING SITE FOR RESIDUE VN4 A 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RBK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2RBK)

(-) 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:261
 aligned with Q8A090_BACTN | Q8A090 from UniProtKB/TrEMBL  Length:261

    Alignment length:261
                                    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 
         Q8A090_BACTN     1 MTKALFFDIDGTLVSFETHRIPSSTIEALEAAHAKGLKIFIATGRPKAIINNLSELQDRNLIDGYITMNGAYCFVGEEVIYKSAIPQEEVKAMAAFCEKKGVPCIFVEEHNISVCQPNEMVKKIFYDFLHVNVIPTVSFEEASNKEVIQMTPFITEEEEKEVLPSIPTCEIGRWYPAFADVTAKGDTKQKGIDEIIRHFGIKLEETMSFGDGGNDISMLRHAAIGVAMGQAKEDVKAAADYVTAPIDEDGISKAMKHFGII 261
               SCOP domains d2rbka_ A: Sugar-phosphate phosphatase BT4131                                                                                                                                                                                                                         SCOP domains
               CATH domains 2rbkA01 A:1-83,A:185-261  [code=3.40.50.1000, no name defined]                     -----------------------------------------------------------------------------------------------------2rbkA01 A:1-83,A:185-261  [code=3.40.50.1000, no name defined]                CATH domains
               Pfam domains ----Hydrolase_3-2rbkA01 A:5-255                                                                                                                                                                                                                                ------ Pfam domains
         Sec.struct. author ...eeee..............hhhhhhhhhhhhhh..eeeee...hhhhh..hhhhhhh....eeeehhh.eeee..eeeee...hhhhhhhhhhhhhhhh..eeee....eeee..hhhhhhhh............hhhhhhh....eeee..hhhhhhhhhhhh...eee.......eee....hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeee....hhhhhhhh.ee..hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rbk A   1 MTKALFFDIDGTLVSFETHRIPSSTIEALEAAHAKGLKIFIATGRPKAIINNLSELQDRNLIDGYITMNGAYCFVGEEVIYKSAIPQEEVKAMAAFCEKKGVPCIFVEEHNISVCQPNEMVKKIFYDFLHVNVIPTVSFEEASNKEVIQMTPFITEEEEKEVLPSIPTCEIGRWYPAFADVTAKGDTKQKGIDEIIRHFGIKLEETMSFGDGGNDISMLRHAAIGVAMGQAKEDVKAAADYVTAPIDEDGISKAMKHFGII 261
                                    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
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8A090_BACTN | Q8A090)
molecular function
    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:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0044283    small molecule biosynthetic process    The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    VN4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2rbk)
 

(-) 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
  2rbk
    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
  Q8A090_BACTN | Q8A090
    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
  Q8A090_BACTN | Q8A090
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8A090_BACTN | Q8A090: 1ymq 2rar 2rav 2rb5

(-) Related Entries Specified in the PDB File

1ymq THE SAME PROTEIN COMPLEXED WITH METAVANADATE.
2rar
2rav
2rb5