1HEW

REFINEMENT OF AN ENZYME COMPLEX WITH INHIBITOR BOUND AT PARTIAL OCCUPANCY. HEN EGG-WHITE LYSOZYME AND TRI-N-ACETYLCHITOTRIOSE AT 1.75 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Refinement of an enzyme complex with inhibitor bound at partial occupancy. Hen egg-white lysozyme and tri-N-acetylchitotriose at 1.75 A resolution.

Cheetham, J.C.Artymiuk, P.J.Phillips, D.C.

(1992) J.Mol.Biol. 224: 613-628


  • PubMed Abstract: 
  • The structure of the tri-N-acetylchitotriose inhibitor complex of hen egg-white lysozyme has been refined at 1.75 A resolution, using data collected from a complex crystal with ligand bound at less than full occupancy. To determine the exact value of ...

    The structure of the tri-N-acetylchitotriose inhibitor complex of hen egg-white lysozyme has been refined at 1.75 A resolution, using data collected from a complex crystal with ligand bound at less than full occupancy. To determine the exact value of the inhibitor occupancy, a model comprising unliganded and sugar-bound protein molecules was generated and refined against the 1.75 A data, using a modified version of the Hendrickson & Konnert least-squares procedure. The crystallographic R-factor for the model was found to fall to a minimum at 55% bound sugar. Conventional refinement assuming unit occupancy was found to yield incorrect thermal and positional parameters. Application of the same refinement procedures to an earlier 2.0 A data set, collected independently on different complex crystals by Blake et al. gave less consistent results than the 1.75 A refinement. From an analysis of the high resolution structure a detailed picture of the protein-carbohydrate interactions in the non-productive complex has emerged, together with the conformation and mobility changes that accompany ligand binding. The specificity of interaction between the protein and inhibitor, bound in subsites A to C of the active site, is seen to be generated primarily by an extensive network of hydrogen bonds, both to the protein itself and to bound solvent molecules. The latter also play an important role in maintaining the structural integrity of the active site cleft in the apo-protein.


    Related Citations: 
    • Crystallographic Studies of the Activity of Hen Egg-White Lysozyme
      Blake, C.C.F.,Johnson, L.N.,Mair, G.A.,North, A.C.T.,Phillips, D.C.,Sarma, V.R.
      (1967) Proc.R.Soc.London,Ser.B 167: 378
    • Protein-Oligosaccharide Interactions: Lysozyme, Phosphorylase, Amylases
      Johnson, L.N.,Cheetham, J.C.,Mclaughlin, P.J.,Acharya, K.R.,Barford, D.,Phillips, D.C.
      (1988) Curr.Top.Microbiol.Immunol. 139: 81
    • On the Conformation of the Hen Egg-White Lysozyme Molecule
      Blake, C.C.F.,Mair, G.A.,North, A.C.T.,Phillips, D.C.,Sarma, V.R.
      (1967) Proc.R.Soc.London,Ser.B 167: 365


    Organizational Affiliation

    Laboratory of Molecular Biophysics, University of Oxford, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEN EGG WHITE LYSOZYME
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.860α = 90.00
b = 78.860β = 90.00
c = 38.250γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other