Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18945.66 
• Atom Count: 1309 
• Residue Count: 164 
• Unique protein chains: 1

184L

SPECIFICITY OF LIGAND BINDING IN A BURIED NON-POLAR CAVITY OF T4 LYSOZYME: LINKAGE OF DYNAMICS AND STRUCTURAL PLASTICITY

• DOI: 10.2210/pdb184L/pdb

• Classification: HYDROLASE (O-GLYCOSYL)
• Organism(s): Enterobacteria phage T4


• Deposited: 1995-04-19 Released: 1995-07-10 
• Deposition Author(s): Morton, A., Matthews, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å

Literature

Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity.

Morton, A., Matthews, B.W.

(1995) Biochemistry 34: 8576-8588

• PubMed: 7612599 
• Primary Citation of Related Structures:  
  1NHB, 188L, 187L, 186L, 185L, 183L, 182L, 181L


• PubMed Abstract: 
  

To better understand the role of shape complementarity in ligand binding and protein core interactions, the structures have been determined of a set of ligands bound within a cavity-containing mutant of T4 lysozyme. The interior cavity is seen to consist of two parts that respond very differently to the binding of ligands. First, there is a relatively rigid region that does not relax significantly upon binding any ligand. Second, there is a more flexible region that moves to various extents in response to binding the different ligands. The part of the binding site that remains rigid is characterized by low temperature factors and strong protection from hydrogen exchange. This part of the site appears to be primarily responsible for discriminating between ligands of different shape (i.e., for determining specificity). The more flexible region, characterized by relatively high temperature factors and weak protection from hydrogen exchange, allows some promiscuity in binding by undergoing variable amounts of deformation at essentially the same energetic cost. This linkage between the dynamic information represented by crystallographic temperature factors and hydrogen-exchange behavior on the one hand, and structural plasticity in response to ligand binding on the other hand, suggests a way to improve our understanding of steric interactions in protein cores and protein-ligand binding sites. Ligand design and packing algorithms might take advantage of this information, requiring complementary interactions where the protein is rigid and allowing some overlap in regions where the protein is flexible.

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Related Citations: 

• Energetic Origins of Specificity of Ligand Binding in an Interior Cavity of T4 Lysozyme
  Morton, A.,Baase, W.A.,Matthews, B.W.
  () TO BE PUBLISHED --: --
• Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstroms Resolution
  Weaver, L.H.,Matthews, B.W.
  (1987) J.Mol.Biol. 193: 189




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Organizational Affiliation: 

Institute of Molecular Biology, Howard Hughes Medical Institute, Eugene, Oregon, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
T4 LYSOZYME	A	164	Enterobacteria phage T4	Mutation(s): 0  Gene Names: E EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4) Go to UniProtKB:  P00720

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
HED	A	2-HYDROXYETHYL DISULFIDE C4 H10 O2 S2 KYNFOMQIXZUKRK-UHFFFAOYSA-N
I4B	A	ISOBUTYLBENZENE C10 H14 KXUHSQYYJYAXGZ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
I4B	Kd: 19000 nM (97) BINDINGDB
I4B	Ka: 51000 M-1 BINDINGMOAD
I4B	Kd: 19000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 60.900	α = 90.00
b = 60.900	β = 90.00
c = 97.300	γ = 120.00

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-04-19 
• Released Date: 1995-07-10 
• Deposition Author(s): Morton, A., Matthews, B.W.

Revision History 

• Version 1.0: 1995-07-10
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-11-29
  Type: Derived calculations, Other