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
  • Alignments of the sequence of 2YBE with the sequences similar proteins can be viewed for 2YBE'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 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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