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 :  2.6 ANGSTROM CRYSTAL STRUCTURE OF PUTATIVE PHOSPHOGLYCERATE MUTASE 1 FROM TOXOPLASMA GONDII
 
Authors :  G. Minasov, J. Ruan, H. Ngo, L. Shuvalova, I. Dubrovska, K. Flores, D. Sh D. Roos, W. F. Anderson, Center For Structural Genomics Of Infec Diseases (Csgid)
Date :  10 Jan 14  (Deposition) - 22 Jan 14  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Csgid, Phosphoglycerate Mutase-Like, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, J. Ruan, H. Ngo, L. Shuvalova, I. Dubrovska, K. Flores, D. Shanmugam, D. Roos, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
2. 6 Angstrom Crystal Structure Of Putative Phosphoglycerate Mutase 1 From Toxoplasma Gondii.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHOGLYCERATE MUTASE PGMII
    Chains: A, B, C, D
    EC Number: 5.4.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG28
    Expression System Strain: BL21(DE3)/PMAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 75-339
    Gene: PGMII, TGME49_297060
    Organism Scientific: TOXOPLASMA GONDII
    Organism Taxid: 508771
    Strain: ME49

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NA4Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:155 , LYS A:156 , VAL A:158 , ASN A:160 , HOH A:410BINDING SITE FOR RESIDUE NA A 301
2AC2SOFTWARETYR B:155 , VAL B:158 , ASN B:160 , LEU B:163 , HOH B:438 , HOH B:451BINDING SITE FOR RESIDUE NA B 301
3AC3SOFTWARETYR C:155 , VAL C:158 , ASN C:160 , LEU C:163 , HOH C:417BINDING SITE FOR RESIDUE NA C 301
4AC4SOFTWARETYR D:155 , VAL D:158 , ASN D:160BINDING SITE FOR RESIDUE NA D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ODI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ODI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ODI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ODI)

(-) Exons   (0, 0)

(no "Exon" information available for 4ODI)

(-) 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:246
                                                                                                                                                                                                                                                                                      
               SCOP domains d4odia_ A: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeee...hhhhhh...........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhh.....eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh....hhhhh........eeeee.....eeeeee..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4odi A  12 GNMAKAKYTLVLIRHGESTWNKENRFTGWTDVPLSPVGEQEAVEAAKALKEKGFEFDVAYTSVLQRAVVTCWTVLKGTDMCHIPVKSSWRLNERHYGALQGLNKAETAAKHGDEQVKIWRRSYDIPPPPLEKSDKRWPGNDAVYKMVPNEALPLTECLKDTVERVLPFWFDHIAPSIMEGKRVLVAAHGNSLRGLVKHLDKMSDEAVLELNIPTGVPLVYELDEDLQPVRHYYLLDEAELKAKMEA 257
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      


Chain B from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains d4odib_ B: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...hhhhhh...........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhh.....eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh....hhhhh........eeeee.....eeeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4odi B  15 AKAKYTLVLIRHGESTWNKENRFTGWTDVPLSPVGEQEAVEAAKALKEKGFEFDVAYTSVLQRAVVTCWTVLKGTDMCHIPVKSSWRLNERHYGALQGLNKAETAAKHGDEQVKIWRRSYDIPPPPLEKSDKRWPGNDAVYKMVPNEALPLTECLKDTVERVLPFWFDHIAPSIMEGKRVLVAAHGNSLRGLVKHLDKMSDEAVLELNIPTGVPLVYELDEDLQPVRHYYLLDEAELKAKMEAVA 259
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254     


Chain C from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains d4odic_ C: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...hhhhhh...........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhh.....eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh....hhhhh........eeeee.....eeeeee..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4odi C  15 AKAKYTLVLIRHGESTWNKENRFTGWTDVPLSPVGEQEAVEAAKALKEKGFEFDVAYTSVLQRAVVTCWTVLKGTDMCHIPVKSSWRLNERHYGALQGLNKAETAAKHGDEQVKIWRRSYDIPPPPLEKSDKRWPGNDAVYKMVPNEALPLTECLKDTVERVLPFWFDHIAPSIMEGKRVLVAAHGNSLRGLVKHLDKMSDEAVLELNIPTGVPLVYELDEDLQPVRHYYLLDEAELKAKMEA 257
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254   


Chain D from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                        
               SCOP domains d4odid_ D: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhh...........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhh.....eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh....hhhhh........eeeee.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4odi D  17 AKYTLVLIRHGESTWNKENRFTGWTDVPLSPVGEQEAVEAAKALKEKGFEFDVAYTSVLQRAVVTCWTVLKGTDMCHIPVKSSWRLNERHYGALQGLNKAETAAKHGDEQVKIWRRSYDIPPPPLEKSDKRWPGNDAVYKMVPNEALPLTECLKDTVERVLPFWFDHIAPSIMEGKRVLVAAHGNSLRGLVKHLDKMSDEAVLELNIPTGVPLVYELDEDLQPVRHYYLLDE 248
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ODI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ODI)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4odi)
 

(-) 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
  4odi
    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
  S8GJT7_TOXGM | S8GJT7
    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)
  5.4.2.4
    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
  S8GJT7_TOXGM | S8GJT7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4ODI)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4ODI)