2Y3I Transferase date Dec 21, 2010
title The Structure Of The Fully Closed Conformation Of Human Pgk In Complex With L-Adp, 3pg And The Tsa Aluminium Tetrafluoride
authors M.W.Bowler, L.Chaloin, C.Lionne
compound source
Molecule: Phosphoglycerate Kinase 1
Chain: A, D
Fragment: Residues 1-416
Synonym: Phosphoglycerate Kinase, Cell Migration-Inducing G Protein, Primer Recognition Protein 2, Prp 2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
symmetry Space Group: P 21 21 21
R_factor 0.26266 R_Free 0.30322
length a length b length c angle alpha angle beta angle gamma
38.419 103.877 203.094 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand 3PG, ALF, CL, LA8, MG enzyme Transferase E.C. BRENDA
A, D

Primary referenceInteraction of human 3-phosphoglycerate kinase with its two substrates: is substrate antagonism a kinetic advantage?, Lallemand P, Chaloin L, Roy B, Barman T, Bowler MW, Lionne C, J Mol Biol. 2011 Jun 24;409(5):742-57. Epub 2011 Apr 27. PMID:21549713
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (201 Kb) [Save to disk]
  • Biological Unit Coordinates (2y3i.pdb1.gz) 132 Kb
  • Biological Unit Coordinates (2y3i.pdb2.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 2Y3I
  • CSU: Contacts of Structural Units for 2Y3I
  • Structure Factors (852 Kb)
  • Retrieve 2Y3I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Y3I from S2C, [Save to disk]
  • Re-refined 2y3i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2Y3I 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 2Y3I
  • 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 2Y3I, from MSDmotif at EBI
  • Fold representative 2y3i from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2y3i_D] [2y3i] [2y3i_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2Y3I
  • Community annotation for 2Y3I 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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