Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19018.73 
• Atom Count: 1483 
• Residue Count: 164 
• Unique protein chains: 1

3HUA

4,5,6,7-tetrahydroindole in complex with T4 lysozyme L99A/M102Q

• DOI: 10.2210/pdb3HUA/pdb

• Classification: HYDROLASE
• Organism(s): Enterobacteria phage T4
• Expression System: Escherichia coli
• Mutation(s): 4 


• Deposited: 2009-06-13 Released: 2009-11-03 
• Deposition Author(s): Boyce, S.E., Mobley, D.L., Rocklin, G.J., Graves, A.P., Dill, K.A., Shoichet, B.K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.4 Å
• R-Value Free: 0.192 
• R-Value Work: 0.173 

Literature

Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.

Boyce, S.E., Mobley, D.L., Rocklin, G.J., Graves, A.P., Dill, K.A., Shoichet, B.K.

(2009) J.Mol.Biol. 394: 747-763

• PubMed: 19782087 
• DOI: 10.1016/j.jmb.2009.09.049
• Primary Citation of Related Structures:  
  3HUQ, 3HUK, 3HU9, 3HU8, 3HTG, 3HTF, 3HTD, 3HTB, 3HT9, 3HT8, 3HT7, 3HT6


• PubMed Abstract: 
  

We present a combined experimental and modeling study of organic ligand molecules binding to a slightly polar engineered cavity site in T4 lysozyme (L99A/M102Q). For modeling, we computed alchemical absolute binding free energies. These were blind tests performed prospectively on 13 diverse, previously untested candidate ligand molecules. We predicted that eight compounds would bind to the cavity and five would not; 11 of 13 predictions were correct at this level. The RMS error to the measurable absolute binding energies was 1.8 kcal/mol. In addition, we computed "relative" binding free energies for six phenol derivatives starting from two known ligands: phenol and catechol. The average RMS error in the relative free energy prediction was 2.5 kcal/mol (phenol) and 1.1 kcal/mol (catechol). To understand these results at atomic resolution, we obtained x-ray co-complex structures for nine of the diverse ligands and for all six phenol analogs. The average RMSD of the predicted pose to the experiment was 2.0 A (diverse set), 1.8 A (phenol-derived predictions), and 1.2 A (catechol-derived predictions). We found that predicting accurate affinities and rank-orderings required near-native starting orientations of the ligand in the binding site. Unanticipated binding modes, multiple ligand binding, and protein conformational change all proved challenging for the free energy methods. We believe that these results can help guide future improvements in physics-based absolute binding free energy methods.

---

Organizational Affiliation: 

Graduate Group in Chemistry and Chemical Biology, University of California-San Francisco, San Francisco, CA 94158-2518, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysozyme	A	164	Enterobacteria phage T4	Mutations: A99L, D38S, D144N, Q102M 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
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
JZ9	A	4,5,6,7-tetrahydro-1H-indole C8 H11 N KQBVVLOYXDVATK-UHFFFAOYSA-N
BME	A	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
JZ9	Kd: 278000 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.4 Å
• R-Value Free: 0.192 
• R-Value Work: 0.173 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 60.327	α = 90.00
b = 60.327	β = 90.00
c = 97.438	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-06-13 
• Released Date: 2009-11-03 
• Deposition Author(s): Boyce, S.E., Mobley, D.L., Rocklin, G.J., Graves, A.P., Dill, K.A., Shoichet, B.K.

Revision History 

• Version 1.0: 2009-11-03
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-11-01
  Type: Refinement description