5ES3 | pdb_00005es3

Co-crystal structure of LDH liganded with oxamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.203 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

A Streamlined, Automated Protocol for the Production of Milligram Quantities of Untagged Recombinant Rat Lactate Dehydrogenase A Using AKTAxpressTM.

Nowicki, M.W.Blackburn, E.A.McNae, I.W.Wear, M.A.

(2015) PLoS One 10: e0146164-e0146164

  • DOI: https://doi.org/10.1371/journal.pone.0146164
  • Primary Citation Related Structures: 
    5ES3

  • PubMed Abstract: 

    We developed an efficient, automated 2-step purification protocol for the production of milligram quantities of untagged recombinant rat lactate dehydrogenase A (rLDHA) from E. coli, using the ÄKTAxpress™ chromatography system. Cation exchange followed by size exclusion results in average final purity in excess of 93% and yields ~ 14 milligrams per 50 ml of original cell culture in EnPresso B media, in under 8 hrs, including all primary sample processing and column equilibration steps. The protein is highly active and coherent biophysically and a viable alternative to the more problematic human homolog for structural and ligand-binding studies; an apo structure of untagged rLDHA was solved to a resolution 2.29 Å (PDB ID 5ES3). Our automated methodology uses generic commercially available pre-packed columns and simple buffers, and represents a robust standard method for the production of milligram amounts of untagged rLDHA, facilitating a novel fragment screening approach for new inhibitors.


  • Organizational Affiliation
    • The Edinburgh Protein Production Facility (EPPF), Wellcome Trust Centre for Cell Biology (WTCCB), University of Edinburgh, King's Buildings, Max Born Crescent, Mayfield Road, Edinburgh, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 291.62 kDa 
  • Atom Count: 21,636 
  • Modeled Residue Count: 2,625 
  • Deposited Residue Count: 2,648 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
L-lactate dehydrogenase A chain331Rattus norvegicusMutation(s): 0 
Gene Names: LdhaLdh-1Ldh1
EC: 1.1.1.27
UniProt
Find proteins for P04642 (Rattus norvegicus)
Explore P04642 
Go to UniProtKB:  P04642
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04642
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
OXM BindingDB:  5ES3 Ki: min: 2.60e+4, max: 1.38e+5 (nM) from 3 assay(s)
IC50: min: 5.72e+4, max: 8.00e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.08α = 90
b = 146.63β = 90
c = 284.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description