Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 35.60 kDa 
• Atom Count: 3013 
• Modelled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

4N66

Thermolysin in complex with UBTLN37

• PDB DOI: 10.2210/pdb4N66/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Bacillus thermoproteolyticus
• Mutation(s): No 


• Deposited: 2013-10-11 Released: 2014-04-02 
• Deposition Author(s): Krimmer, S.G., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.145 
• R-Value Work: 0.112 
• R-Value Observed: 0.114 

Literature

Methyl, Ethyl, Propyl, Butyl: Futile But Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors.

Krimmer, S.G., Betz, M., Heine, A., Klebe, G.

(2014) ChemMedChem 4: 833-846

• PubMed: 24623396 
• DOI: 10.1002/cmdc.201400013
• Primary Citation of Related Structures:  
  4MTW, 4MWP, 4MXJ, 4MZN, 4N4E, 4N5P, 4N66, 4OI5


• PubMed Abstract: 
  

Water is ubiquitously present in any biological system and has therefore to be regarded as an additional binding partner in the protein-ligand binding process. Upon complex formation, a new solvent-exposed surface is generated and water molecules from the first solvation layer will arrange around this newly formed surface. So far, the influence of such water arrangements on the ligand binding properties is unknown. In this study, the binding modes of nine congeneric phosphonamidate-type inhibitors with systematically varied, size-increasing hydrophobic P2 ' substituents (from methyl to phenylethyl) addressing the hydrophobic, solvent-exposed S2 ' pocket of thermolysin were analyzed by high-resolution crystal structures and correlated with their thermodynamic binding profiles as measured by isothermal titration calorimetry. Overall, ΔΔG spreads over 7.0 kJ mol(-1) , ΔΔH varies by 15.8 kJ mol(-1) , and -TΔΔS by 12.1 kJ mol(-1) . Throughout the series, these changes correlate remarkably well with the geometric differences of water molecules arranged adjacent to the P2 ' substituents. Ligands with medium-sized P2 ' substituents exhibit highest affinities, presumably because of their optimal solvation patterns around these complexes. The addition, removal, or rearrangement of even a single methyl group can result in a strong modulation of the adjacent water network pattern shifting from enthalpy to entropy-driven binding. In conclusion, the quality of a water network assembled around a protein-ligand complex influences the enthalpy/entropy signature and can even modulate affinity to a surprising extent.

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Organizational Affiliation: 

Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg (Germany).

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermolysin	A [auth E]	316	Bacillus thermoproteolyticus	Mutation(s): 0  Gene Names: npr EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus) Explore P00800  Go to UniProtKB:  P00800

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2GZ	N [auth E]	P-((((benzyloxy)carbonyl)amino)methyl)-N-((S)-4-methyl-1-(neopentylamino)-1-oxopentan-2-yl)phosphonamidic acid C20 H34 N3 O5 P GRURGYQNFDMDDQ-KRWDZBQOSA-N
GOL	K [auth E], L [auth E], M [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	G [auth E], H [auth E], I [auth E], J [auth E]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	C [auth E], D [auth E], E, F [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 6
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001182 (2GZ)	N [auth E]	N~2~-[(S)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-(2,2-DIMETHYLPROPYL)-L-LEUCINAMIDE	Peptide-like / Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.145 
• R-Value Work: 0.112 
• R-Value Observed: 0.114 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.171	α = 90
b = 92.171	β = 90
c = 130.104	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-10-11 
• Released Date: 2014-04-02 
Deposition Author(s): Krimmer, S.G., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2014-04-16
  Changes: Database references