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
  • Alignments of the sequence of 2Y3I with the sequences similar proteins can be viewed for 2Y3I's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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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