3C39 Transferase date Jan 28, 2008
title Crystal Structure Of Human Phosphoglycerate Kinase Bound To 3-Phosphoglycerate
authors S.T.Arold, C.Gondeau, C.Lionne, L.Chaloin
compound source
Molecule: Phosphoglycerate Kinase 1
Chain: A, B
Synonym: 3-Phosphoglycerate Kinase, Primer Recognition Protein 2, Prp 2, Cell Migration-Inducing Gene 10 Protein;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pgk1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)Pdia17
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: P 1
R_factor 0.191 R_Free 0.273
length a length b length c angle alpha angle beta angle gamma
35.616 55.790 93.230 79.18 84.33 83.23
method X-Ray Diffractionresolution 1.85 Å
ligand 3PG enzyme Transferase E.C. BRENDA
A, B

Primary referenceMolecular basis for the lack of enantioselectivity of human 3-phosphoglycerate kinase., Gondeau C, Chaloin L, Lallemand P, Roy B, Perigaud C, Barman T, Varga A, Vas M, Lionne C, Arold ST, Nucleic Acids Res. 2008 Jun;36(11):3620-9. Epub 2008 May 7. PMID:18463139
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (135 Kb) [Save to disk]
  • Biological Unit Coordinates (3c39.pdb1.gz) 67 Kb
  • Biological Unit Coordinates (3c39.pdb2.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 3C39
  • CSU: Contacts of Structural Units for 3C39
  • Likely Quarternary Molecular Structure file(s) for 3C39
  • Structure Factors (402 Kb)
  • Retrieve 3C39 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3C39 from S2C, [Save to disk]
  • Re-refined 3c39 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3C39 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 3C39
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3C39, from MSDmotif at EBI
  • Fold representative 3c39 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3c39_A] [3c39] [3c39_B]
  • SWISS-PROT database: [P00558]
  • Domain organization of [PGK1_HUMAN] by SWISSPFAM
  • Other resources with information on 3C39
  • Community annotation for 3C39 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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