5PGM Isomerase date Aug 19, 1998
title Saccharomyces Cerevisiae Phosphoglycerate Mutase
authors D.J.Rigden, S.E.V.Phillips, L.A.Fothergill-Gilmore
compound source
Molecule: Phosphoglycerate Mutase 1
Chain: D, C, A, B, E, F, G, H
Synonym: Phosphoglyceromutase
Ec: 5.4.2.1
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: S150-Gpm\:\:His3
Cellular_location: Cytoplasm
symmetry Space Group: P 1 21 1
R_factor 0.196 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.497 93.262 147.329 90.00 90.15 90.00
method X-Ray Diffractionresolution 2.12 Å
ligand ALA, SO4 enzyme Isomerase E.C.5.4.2.1 BRENDA
related structures by homologous chain: 1RII, 4PGM
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referenceSulphate ions observed in the 2.12 A structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism., Rigden DJ, Walter RA, Phillips SE, Fothergill-Gilmore LA, J Mol Biol. 1999 Mar 12;286(5):1507-17. PMID:10064712
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (336 Kb) [Save to disk]
  • Biological Unit Coordinates (5pgm.pdb1.gz) 168 Kb
  • Biological Unit Coordinates (5pgm.pdb2.gz) 168 Kb
  • LPC: Ligand-Protein Contacts for 5PGM
  • CSU: Contacts of Structural Units for 5PGM
  • Likely Quarternary Molecular Structure file(s) for 5PGM
  • Structure Factors (2531 Kb)
  • Retrieve 5PGM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5PGM from S2C, [Save to disk]
  • Re-refined 5pgm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5PGM in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5PGM
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 5PGM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d5pgma_, region A [Jmol] [rasmolscript] [script source]
        - Domain d5pgmb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d5pgmc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d5pgmd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d5pgme_, region E [Jmol] [rasmolscript] [script source]
        - Domain d5pgmf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d5pgmg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d5pgmh_, region H [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5pgm_F] [5pgm] [5pgm_H] [5pgm_G] [5pgm_C] [5pgm_B] [5pgm_A] [5pgm_D] [5pgm_E]
  • SWISS-PROT database: [P00950]
  • Domain organization of [PMG1_YEAST] by SWISSPFAM
  • Domain found in 5PGM: [PGAM ] by SMART
    • Other resources with information on 5PGM
  • Community annotation for 5PGM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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