2YBE Transferase date Mar 07, 2011
title The Structure Of The Fully Closed Conformation Of Human Pgk In Complex With L-Adp, 3pg And The Tsa Aluminium Tetrafluoride At 2.0 A Resolution
authors M.W.Bowler, L.Chaloin, C.Lionne
compound source
Molecule: Phosphoglycerate Kinase 1
Chain: A
Synonym: Phosphoglycerate Kinase, Cell Migration-Inducing G Protein, Primer Recognition Protein 2, Prp 2;
Ec: 2.7.2.3
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 0.19316 R_Free 0.24329
crystal
cell
length a length b length c angle alpha angle beta angle gamma
39.202 91.030 108.807 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 3PG, ALF, CL, LA8, MG enzyme Transferase E.C.2.7.2.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


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] (139 Kb) [Save to disk]
  • Biological Unit Coordinates (2ybe.pdb1.gz) 134 Kb
  • LPC: Ligand-Protein Contacts for 2YBE
  • CSU: Contacts of Structural Units for 2YBE
  • Structure Factors (1265 Kb)
  • Retrieve 2YBE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YBE from S2C, [Save to disk]
  • Re-refined 2ybe structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YBE 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 2YBE
  • 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 2YBE, from MSDmotif at EBI
  • Fold representative 2ybe from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ybe] [2ybe_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2YBE
  • Community annotation for 2YBE 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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