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: 18711.20 
• Atom Count: 1315 
• Residue Count: 162 
• Unique protein chains: 1

2OU0

1-methylpyrrole in complex with T4 Lysozyme L99A

• DOI: 10.2210/pdb2OU0/pdb

• Classification: HYDROLASE
• Organism(s): Enterobacteria phage T4
• Expression System: Escherichia coli
• Mutation(s): 3 


• Deposited: 2007-02-09 Released: 2007-08-07 
• Deposition Author(s): Graves, A.P., Shoichet, B.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.234 
• R-Value Work: 0.191 

Literature

Predicting absolute ligand binding free energies to a simple model site.

Mobley, D.L., Graves, A.P., Chodera, J.D., McReynolds, A.C., Shoichet, B.K., Dill, K.A.

(2007) J.Mol.Biol. 371: 1118-1134

• PubMed: 17599350 
• DOI: 10.1016/j.jmb.2007.06.002
• Primary Citation of Related Structures:  
  2OTZ, 2OTY


• PubMed Abstract: 
  

A central challenge in structure-based ligand design is the accurate prediction of binding free energies. Here we apply alchemical free energy calculations in explicit solvent to predict ligand binding in a model cavity in T4 lysozyme. Even in this simple site, there are challenges. We made systematic improvements, beginning with single poses from docking, then including multiple poses, additional protein conformational changes, and using an improved charge model. Computed absolute binding free energies had an RMS error of 1.9 kcal/mol relative to previously determined experimental values. In blind prospective tests, the methods correctly discriminated between several true ligands and decoys in a set of putative binders identified by docking. In these prospective tests, the RMS error in predicted binding free energies relative to those subsequently determined experimentally was only 0.6 kcal/mol. X-ray crystal structures of the new ligands bound in the cavity corresponded closely to predictions from the free energy calculations, but sometimes differed from those predicted by docking. Finally, we examined the impact of holding the protein rigid, as in docking, with a view to learning how approximations made in docking affect accuracy and how they may be improved.

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Organizational Affiliation: 

Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143-2518, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysozyme	X	162	Enterobacteria phage T4	Mutation(s): 3  Gene Names: E EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4) Go to UniProtKB:  P00720

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	X	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MR3	X	1-METHYL-1H-PYRROLE C5 H7 N OXHNLMTVIGZXSG-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
MR3	Kd: 592000 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.234 
• R-Value Work: 0.191 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 60.205	α = 90.00
b = 60.205	β = 90.00
c = 96.372	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	phasing
REFMAC	refinement
SCALEPACK	data scaling
DENZO	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-02-09 
• Released Date: 2007-08-07 
• Deposition Author(s): Graves, A.P., Shoichet, B.K.

Revision History 

• Version 1.0: 2007-08-07
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-10-18
  Type: Refinement description