2XE8 Transferase date May 11, 2010
title The Complete Reaction Cycle Of Human Phosphoglycerate Kinase: The Open Ternary Complex With 3pg And Amp-Pnp
authors M.J.Cliff, N.J.Baxter, G.M.Blackburn, A.Merli, M.Vas, J.P.Waltho, M.W.Bowler
compound source
Molecule: Phosphoglycerate Kinase 1
Chain: A
Synonym: Primer Recognition Protein 2, Prp 2, Cell Migration-Inducing Gene 10 Protein;
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
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22a
symmetry Space Group: P 21 21 2
R_factor 0.19816 R_Free 0.24252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.320 71.170 91.470 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.79 Å
ligand 3PG, ACP enzyme Transferase E.C.2.7.2.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA Spring-loaded Release Mechanism Regulates Domain Movement and Catalysis in Phosphoglycerate Kinase., Zerrad L, Merli A, Schroder GF, Varga A, Graczer E, Pernot P, Round A, Vas M, Bowler MW, J Biol Chem. 2011 Apr 22;286(16):14040-8. Epub 2011 Feb 24. PMID:21349853
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (135 Kb) [Save to disk]
  • Biological Unit Coordinates (2xe8.pdb1.gz) 130 Kb
  • LPC: Ligand-Protein Contacts for 2XE8
  • CSU: Contacts of Structural Units for 2XE8
  • Structure Factors (1720 Kb)
  • Retrieve 2XE8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XE8 from S2C, [Save to disk]
  • Re-refined 2xe8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XE8 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 2XE8
  • 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 2XE8, from MSDmotif at EBI
  • Fold representative 2xe8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xe8] [2xe8_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 2XE8 with the sequences similar proteins can be viewed for 2XE8'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 2XE8
  • Community annotation for 2XE8 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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