Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  Y92C CATALYTIC RESIDUE MUTANT OF PHOSPHOGLYCERATE MUTASE FROM PLASMODIUM FALCIPARUM
 
Authors :  E. T. Larson, E. A. Merritt, Medical Structural Genomics Of Pathog Protozoa
Date :  05 Nov 09  (Deposition) - 17 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Pgam, Glycolysis, Malaria, Structural Genomics, Medical Structural Genomics Of Pathogenic Protozoa, Msgpp, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. T. Larson, J. M. Caruthers, L. Zhang, W. G. J. Hol, E. A. Merritt
Structure Of A Phosphoglycerate Mutase From Plasmodium Falciparum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHOGLYCERATE MUTASE
    Chains: A, B, C, D
    EC Number: 5.4.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BG1861
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PF11_0208
    Mutation: YES
    Organism Scientific: PLASMODIUM FALCIPARUM 3D7
    Organism Taxid: 36329

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3KKK)

(-) Sites  (0, 0)

(no "Site" information available for 3KKK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KKK)

(-) 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:230
 aligned with Q8IIG6_PLAF7 | Q8IIG6 from UniProtKB/TrEMBL  Length:250

    Alignment length:230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
         Q8IIG6_PLAF7     2 TTYTLVLLRHGESTWNKENKFTGWTDVPLSEKGEEEAIAAGKYLKEKNFKFDVVYTSVLKRAICTAWNVLKTADLLHVPVVKTWRLNERHYGSLQGLNKSETAKKYGEEQVKIWRRSYDIPPPKLDKEDNRWPGHNVVYKNVPKDALPFTECLKDTVERVLPFWFDHIAPDILANKKVMVAAHGNSLRGLVKHLDNLSEADVLELNIPTGVPLVYELDENLKPIKHYYLL 231
               SCOP domains d3kkka_ A: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains 3kkkA00 A:2-231 Phosphoglycerate mutase-like                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhh...........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhh.....eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh..hhhhhhhh.......eeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kkk A   2 TTYTLVLLRHGESTWNKENKFTGWTDVPLSEKGEEEAIAAGKYLKEKNFKFDVVYTSVLKRAICTAWNVLKTADLLHVPVVKTWRLNERHCGSLQGLNKSETAKKYGEEQVKIWRRSYDIPPPKLDKEDNRWPGHNVVYKNVPKDALPFTECLKDTVERVLPFWFDHIAPDILANKKVMVAAHGNSLRGLVKHLDNLSEADVLELNIPTGVPLVYELDENLKPIKHYYLL 231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231


Chain B from PDB  Type:PROTEIN  Length:231
 aligned with Q8IIG6_PLAF7 | Q8IIG6 from UniProtKB/TrEMBL  Length:250

    Alignment length:231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
         Q8IIG6_PLAF7     1 MTTYTLVLLRHGESTWNKENKFTGWTDVPLSEKGEEEAIAAGKYLKEKNFKFDVVYTSVLKRAICTAWNVLKTADLLHVPVVKTWRLNERHYGSLQGLNKSETAKKYGEEQVKIWRRSYDIPPPKLDKEDNRWPGHNVVYKNVPKDALPFTECLKDTVERVLPFWFDHIAPDILANKKVMVAAHGNSLRGLVKHLDNLSEADVLELNIPTGVPLVYELDENLKPIKHYYLL 231
               SCOP domains d3kkkb_ B: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains 3kkkB00 B:1-231 Phosphoglycerate mutase-like                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhhh...........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhh......eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh..hhhhhhhh.......eeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kkk B   1 MTTYTLVLLRHGESTWNKENKFTGWTDVPLSEKGEEEAIAAGKYLKEKNFKFDVVYTSVLKRAICTAWNVLKTADLLHVPVVKTWRLNERHCGSLQGLNKSETAKKYGEEQVKIWRRSYDIPPPKLDKEDNRWPGHNVVYKNVPKDALPFTECLKDTVERVLPFWFDHIAPDILANKKVMVAAHGNSLRGLVKHLDNLSEADVLELNIPTGVPLVYELDENLKPIKHYYLL 231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 


Chain C from PDB  Type:PROTEIN  Length:230
 aligned with Q8IIG6_PLAF7 | Q8IIG6 from UniProtKB/TrEMBL  Length:250

    Alignment length:230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
         Q8IIG6_PLAF7     2 TTYTLVLLRHGESTWNKENKFTGWTDVPLSEKGEEEAIAAGKYLKEKNFKFDVVYTSVLKRAICTAWNVLKTADLLHVPVVKTWRLNERHYGSLQGLNKSETAKKYGEEQVKIWRRSYDIPPPKLDKEDNRWPGHNVVYKNVPKDALPFTECLKDTVERVLPFWFDHIAPDILANKKVMVAAHGNSLRGLVKHLDNLSEADVLELNIPTGVPLVYELDENLKPIKHYYLL 231
               SCOP domains d3kkkc_ C: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains 3kkkC00 C:2-231 Phosphoglycerate mutase-like                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhh..........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhh.....eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh..hhhhhhhh.......eeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kkk C   2 TTYTLVLLRHGESTWNKENKFTGWTDVPLSEKGEEEAIAAGKYLKEKNFKFDVVYTSVLKRAICTAWNVLKTADLLHVPVVKTWRLNERHCGSLQGLNKSETAKKYGEEQVKIWRRSYDIPPPKLDKEDNRWPGHNVVYKNVPKDALPFTECLKDTVERVLPFWFDHIAPDILANKKVMVAAHGNSLRGLVKHLDNLSEADVLELNIPTGVPLVYELDENLKPIKHYYLL 231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231


Chain D from PDB  Type:PROTEIN  Length:230
 aligned with Q8IIG6_PLAF7 | Q8IIG6 from UniProtKB/TrEMBL  Length:250

    Alignment length:230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
         Q8IIG6_PLAF7     2 TTYTLVLLRHGESTWNKENKFTGWTDVPLSEKGEEEAIAAGKYLKEKNFKFDVVYTSVLKRAICTAWNVLKTADLLHVPVVKTWRLNERHYGSLQGLNKSETAKKYGEEQVKIWRRSYDIPPPKLDKEDNRWPGHNVVYKNVPKDALPFTECLKDTVERVLPFWFDHIAPDILANKKVMVAAHGNSLRGLVKHLDNLSEADVLELNIPTGVPLVYELDENLKPIKHYYLL 231
               SCOP domains d3kkkd_ D: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains 3kkkD00 D:2-231 Phosphoglycerate mutase-like                                                                                                                                                                                           CATH domains
           Pfam domains (1) ---His_Phos_1-3kkkD01 D:5-191                                                                                                                                                                 ---------------------------------------- Pfam domains (1)
           Pfam domains (2) ---His_Phos_1-3kkkD02 D:5-191                                                                                                                                                                 ---------------------------------------- Pfam domains (2)
           Pfam domains (3) ---His_Phos_1-3kkkD03 D:5-191                                                                                                                                                                 ---------------------------------------- Pfam domains (3)
           Pfam domains (4) ---His_Phos_1-3kkkD04 D:5-191                                                                                                                                                                 ---------------------------------------- Pfam domains (4)
         Sec.struct. author .eeeeeeee...hhhhhhh..........hhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhh.....eee.hhhh...hhhhh..hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh..hhhhhhhh.......eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kkk D   2 TTYTLVLLRHGESTWNKENKFTGWTDVPLSEKGEEEAIAAGKYLKEKNFKFDVVYTSVLKRAICTAWNVLKTADLLHVPVVKTWRLNERHCGSLQGLNKSETAKKYGEEQVKIWRRSYDIPPPKLDKEDNRWPGHNVVYKNVPKDALPFTECLKDTVERVLPFWFDHIAPDILANKKVMVAAHGNSLRGLVKHLDNLSEADVLELNIPTGVPLVYELDENLKPIKHYYLL 231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
   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  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: PGM (50)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q8IIG6_PLAF7 | Q8IIG6)
molecular function
    GO:0046538    2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity    Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate; this reaction requires the cofactor 2,3-bisphosphoglycerate.
    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:0016868    intramolecular transferase activity, phosphotransferases    Catalysis of the transfer of a phosphate group from one position to another within a single molecule.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0004619    phosphoglycerate mutase activity    Catalysis of the reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate.
biological process
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0043456    regulation of pentose-phosphate shunt    Any process that modulates the frequency, rate or extent of the pentose-phosphate shunt, the process in which glucose is oxidized, coupled to NADPH synthesis.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 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
(no "Ligands, Modified Residues, Ions" information available for 3kkk)
 
  Sites
(no "Sites" information available for 3kkk)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3kkk)
 

(-) 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 ](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
  3kkk
    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
  Q8IIG6_PLAF7 | Q8IIG6
    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)
  5.4.2.1
    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
  Q8IIG6_PLAF7 | Q8IIG6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8IIG6_PLAF7 | Q8IIG6: 1xq9

(-) Related Entries Specified in the PDB File

1xq9 STRUCTURE OF PHOSPHOGLYCERATE MUTASE FROM PLASMODIUM FALCIPARUM AT 2.6 RESOLUTION RELATED ID: PFAL005984AAA RELATED DB: TARGETDB