Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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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: 18796.13 
• Atom Count: 1387 
• Residue Count: 164 
• Unique protein chains: 1

5JWU

T4 Lysozyme L99A/M102Q with 1,2-Dihydro-1,2-azaborine Bound

• DOI: 10.2210/pdb5JWU/pdb

• Classification: HYDROLASE
• Organism(s): Enterobacteria phage T4
• Expression System: Escherichia coli
• Mutation(s): 6 


• Deposited: 2016-05-12 Released: 2016-09-21 
• Deposition Author(s): Lee, H., Fischer, M., Shoichet, B.K., Liu, S.-Y.
• Funding Organization(s): National Institutes of Health 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.251 
• R-Value Work: 0.226 

Literature

Hydrogen Bonding of 1,2-Azaborines in the Binding Cavity of T4 Lysozyme Mutants: Structures and Thermodynamics.

Lee, H., Fischer, M., Shoichet, B.K., Liu, S.Y.

(2016) J.Am.Chem.Soc. 138: 12021-12024

• PubMed: 27603116 
• DOI: 10.1021/jacs.6b06566
• Primary Citation of Related Structures:  
  5JWW, 5JWV, 5JWT, 5JWS


• PubMed Abstract: 
  

Protein crystallography and calorimetry were used to characterize the binding of 1,2-azaborines to model cavities in T4 lysozyme in direct comparison to their carbonaceous counterparts. In the apolar L99A cavity, affinity for Ab dropped only slightly versus benzene. In the cavity designed to accommodate a single hydrogen bond (L99A/M102Q), Gln102═O···H-N hydrogen bonding for Ab and BEtAb was observed in the crystallographic complexes. The strength of the hydrogen bonding was estimated as 0.94 and 0.64 kcal/mol for Ab and BEtAb, respectively. This work unambiguously demonstrates that 1,2-azaborines can be readily accommodated in classic aryl recognition pockets and establishes one of 1,2-azaborine's distinguishing features from its carbonaceous isostere benzene: its ability to serve as an NH hydrogen bond donor in a biological setting.

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Organizational Affiliation: 

Department of Chemistry, Boston College , Chestnut Hill, Massachusetts 02467, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Endolysin	A	164	Enterobacteria phage T4	Mutation(s): 6  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
B20	A	1,2-dihydro-1,2-azaborinine 1,2-DIHYDRO-1,2-AZABORINE C4 H6 B N OGZZEGWWYQKMSO-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.251 
• R-Value Work: 0.226 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 60.100	α = 90.00
b = 60.100	β = 90.00
c = 96.770	γ = 120.00

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-05-12 
• Released Date: 2016-09-21 
• Deposition Author(s): Lee, H., Fischer, M., Shoichet, B.K., Liu, S.-Y.

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Funding Organization	Location	Grant Number
National Institutes of Health	United States	5001989

Revision History 

• Version 1.0: 2016-09-21
  Type: Initial release
• Version 1.1: 2016-09-28
  Type: Database references