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 :  THE 3-DIMENSIONAL STRUCTURE OF THE GADOLINIUM DERIVATIVE OF MPGP, THE MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE FROM THERMUS THERMOPHILUS HB27
 
Authors :  S. Goncalves, A. M. Esteves, H. Santos, N. Borges, P. M. Matias
Date :  12 Jul 11  (Deposition) - 19 Oct 11  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Haloalkanoid Acid Dehalogenase-Like Phosphatase, Had-Like Phosphatase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Goncalves, A. M. Esteves, H. Santos, N. Borges, P. M. Matias
The Three-Dimensional Structure Of Mannosyl-3-Phosphoglycerate Phosphatase From Thermus Thermophilus Hb27: A New Member Of The Haloalkanoic Acid Dehalogenase Superfamily.
Biochemistry V. 50 9551 2011
PubMed-ID: 21961705  |  Reference-DOI: 10.1021/BI201171H
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANNOSYL-3-PHOSPHOGLYCERATE PHOSPHATASE
    Chains: A, B
    EC Number: 3.1.3.70
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PKK223-3
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27
    Synonym: MPGP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GD6Ligand/IonGADOLINIUM ATOM

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:6 , ASP A:8 , ASP A:202 , HOH A:2003BINDING SITE FOR RESIDUE GD A 261
2AC2SOFTWAREGLU A:14 , GD A:263BINDING SITE FOR RESIDUE GD A 262
3AC3SOFTWAREGLY A:165 , GD A:262BINDING SITE FOR RESIDUE GD A 263
4AC4SOFTWAREASP A:6 , ASP A:8 , THR A:39 , HOH A:2004BINDING SITE FOR RESIDUE CL A 264
5AC5SOFTWAREASP B:6 , ASP B:8 , ASP B:202 , CL B:264 , HOH B:2002BINDING SITE FOR RESIDUE GD B 261
6AC6SOFTWAREGLY B:165 , GD B:263 , HOH B:2050BINDING SITE FOR RESIDUE GD B 262
7AC7SOFTWAREGLU B:14 , ASP B:202 , SER B:203 , GD B:262 , HOH B:2043BINDING SITE FOR RESIDUE GD B 263
8AC8SOFTWAREASP B:6 , ASP B:8 , THR B:39 , GD B:261 , HOH B:2001 , HOH B:2003BINDING SITE FOR RESIDUE CL B 264

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:53 -Pro A:54
2Pro B:53 -Pro B:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZTY)

(-) 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:252
 aligned with Q72K29_THET2 | Q72K29 from UniProtKB/TrEMBL  Length:259

    Alignment length:252
                                    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  
         Q72K29_THET2     1 MIVFTDLDGTLLDERGELGPAREALERLRALGVPVVPVTAKTRKEVEALGLEPPFIVENGGGLYLPRDWPVRAGRPKGGYRVVSLAWPYRKVRARLREAEALAGRPILGYGDLTAEAVARLTGLSREAARRAKAREYDETLVLCPEEVEAVLEALEAVGLEWTHGGRFYHAAKGADKGRAVARLRALWPDPEEARFAVGLGDSLNDLPLFRAVDLAVYVGRGDPPEGVLATPAPGPEGFRYAVERYLLPRLS 252
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..............hhhhhhhhhhhh...eee....hhhhhhhh.....eeehhh.eeeee........eee..eeeee...hhhhhhhhhhhhhhhhh.....hhh.hhhhhhhhhh.hhhhhhhhhh....ee......hhhhhhhhhhhh..eeee....eeee...hhhhhhhhhhhh..hhhhhh.eeeee.hhhhhhhhhh..eeee..........ee....hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zty A   1 MIVFTDLDGTLLDERGELGPAREALERLRALGVPVVPVTAKTRKEVEALGLEPPFIVENGGGLYLPRDWPVRAGRPKGGYRVVSLAWPYRKVRARLREAEALAGRPILGYGDLTAEAVARLTGLSREAARRAKAREYDETLVLCPEEVEAVLEALEAVGLEWTHGGRFYHAAKGADKGRAVARLRALWPDPEEARFAVGLGDSLNDLPLFRAVDLAVYVGRGDPPEGVLATPAPGPEGFRYAVERYLLPRLS 252
                                    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  


Chain B from PDB  Type:PROTEIN  Length:252
 aligned with Q72K29_THET2 | Q72K29 from UniProtKB/TrEMBL  Length:259

    Alignment length:252
                                    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  
         Q72K29_THET2     1 MIVFTDLDGTLLDERGELGPAREALERLRALGVPVVPVTAKTRKEVEALGLEPPFIVENGGGLYLPRDWPVRAGRPKGGYRVVSLAWPYRKVRARLREAEALAGRPILGYGDLTAEAVARLTGLSREAARRAKAREYDETLVLCPEEVEAVLEALEAVGLEWTHGGRFYHAAKGADKGRAVARLRALWPDPEEARFAVGLGDSLNDLPLFRAVDLAVYVGRGDPPEGVLATPAPGPEGFRYAVERYLLPRLS 252
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.hhhhhh.....hhhhhhhhhhhhhh...eee....hhhhhhhh.....eeehhh.eeeee........ee...eeeee...hhhhhhhhhhhhhhhhh...ee....hhhhhhhhhh.hhhhhhhhhh....eeee.hhhhhhhhhhhhhhh..eeee....eeee...hhhhhhhhhhhh.........eeeee.hhhhhhhhhh..eeee..........ee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zty B   1 MIVFTDLDGTLLDERGELGPAREALERLRALGVPVVPVTAKTRKEVEALGLEPPFIVENGGGLYLPRDWPVRAGRPKGGYRVVSLAWPYRKVRARLREAEALAGRPILGYGDLTAEAVARLTGLSREAARRAKAREYDETLVLCPEEVEAVLEALEAVGLEWTHGGRFYHAAKGADKGRAVARLRALWPDPEEARFAVGLGDSLNDLPLFRAVDLAVYVGRGDPPEGVLATPAPGPEGFRYAVERYLLPRLS 252
                                    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
   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 3ZTY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q72K29_THET2 | Q72K29)
molecular function
    GO:0050531    mannosyl-3-phosphoglycerate phosphatase activity    Catalysis of the reaction: 2-(alpha-D-mannosyl)-3-phosphoglycerate + H(2)O = 2-(alpha-D-mannosyl)-D-glycerate + phosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0051479    mannosylglycerate biosynthetic process    The chemical reactions and pathways resulting in the formation of mannosylglycerate, a very common compatible solute in thermophilic and hyperthermophilic organisms.
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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GD  [ 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 ]
 
  Cis Peptide Bonds
    Pro A:53 - Pro A:54   [ RasMol ]  
    Pro B:53 - Pro B:54   [ 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
  3zty
    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
  Q72K29_THET2 | Q72K29
    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)
  3.1.3.70
    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
  Q72K29_THET2 | Q72K29
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q72K29_THET2 | Q72K29: 3ztw 3zu6 3zup 3zw7 3zwd 3zwk 3zx4 3zx5

(-) Related Entries Specified in the PDB File

3ztw THE 3-DIMENSIONAL STRUCTURE OF APO-MPGP, THE MANNOSYL -3- PHOSPHOGLYCERATE PHOSPHATASE FROM THERMUS THERMOPHILUS HB27 IN ITS APO-FORM
3zu6 THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, IN COMPLEX WITH THE ALPHA- MANNOSYLGLYCERATE AND ORTHOPHOSPHATE REACTION PRODUCTS.
3zup THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, IN COMPLEX WITH THE ALPHA- MANNOSYLGLYCERATE AND ORTHOPHOSPHATE REACTION PRODUCTS.
3zw7 THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, IN COMPLEX WITH THE ALPHA- MANNOSYLGLYCERATE AND METAPHOSPHATE.
3zwd THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, IN COMPLEX WITH THE ALPHA- MANNOSYLGLYCERATE.
3zwk THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, IN COMPLEX WITH THE METAVANADATE
3zx4 THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, IN COMPLEX WITH THE ALPHA- MANNOSYLGLYCERATE,ORTHOPHOSPHATE AND MAGNESIUM
3zx5 THE 3-DIMENSIONAL STRUCTURE OF MPGP FROM THERMUS THERMOPHILUS HB27, COVALENTLY BOUND TO VANADATE AND IN COMPLEX WITH ALPHA- MANNOSYLGLYCERATE AND MAGNESIUM