4W55

T4 Lysozyme L99A with n-Propylbenzene Bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6401 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Homologous ligands accommodated by discrete conformations of a buried cavity.

Merski, M.Fischer, M.Balius, T.E.Eidam, O.Shoichet, B.K.

(2015) Proc.Natl.Acad.Sci.USA 112: 5039-5044

  • DOI: 10.1073/pnas.1500806112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Conformational change in protein-ligand complexes is widely modeled, but the protein accommodation expected on binding a congeneric series of ligands has received less attention. Given their use in medicinal chemistry, there are surprisingly few subs ...

    Conformational change in protein-ligand complexes is widely modeled, but the protein accommodation expected on binding a congeneric series of ligands has received less attention. Given their use in medicinal chemistry, there are surprisingly few substantial series of congeneric ligand complexes in the Protein Data Bank (PDB). Here we determine the structures of eight alkyl benzenes, in single-methylene increases from benzene to n-hexylbenzene, bound to an enclosed cavity in T4 lysozyme. The volume of the apo cavity suffices to accommodate benzene but, even with toluene, larger cavity conformations become observable in the electron density, and over the series two other major conformations are observed. These involve discrete changes in main-chain conformation, expanding the site; few continuous changes in the site are observed. In most structures, two discrete protein conformations are observed simultaneously, and energetic considerations suggest that these conformations are low in energy relative to the ground state. An analysis of 121 lysozyme cavity structures in the PDB finds that these three conformations dominate the previously determined structures, largely modeled in a single conformation. An investigation of the few congeneric series in the PDB suggests that discrete changes are common adaptations to a series of growing ligands. The discrete, but relatively few, conformational states observed here, and their energetic accessibility, may have implications for anticipating protein conformational change in ligand design.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2550.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endolysin
A
172Enterobacteria phage T4Mutation(s): 1 
Gene Names: E
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
3H0
Query on 3H0

Download SDF File 
Download CCD File 
A
propylbenzene
C9 H12
ODLMAHJVESYWTB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3H0Kd: 18000 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6401 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.166 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.320α = 90.00
b = 60.320β = 90.00
c = 96.490γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Cootmodel building
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM59957

Revision History 

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-04-22
    Type: Database references
  • Version 1.2: 2015-05-06
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.4: 2017-11-22
    Type: Refinement description