3T73

Thermolysin In Complex With UBTLN22


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Water makes the difference: rearrangement of water solvation layer triggers non-additivity of functional group contributions in protein-ligand binding.

Biela, A.Betz, M.Heine, A.Klebe, G.

(2012) Chemmedchem 7: 1423-1434

  • DOI: 10.1002/cmdc.201200206
  • Primary Citation of Related Structures:  3T74, 3T8F, 3T8G

  • PubMed Abstract: 
  • The binding of four congeneric peptide-like thermolysin inhibitors has been studied by high-resolution crystal structure analysis and isothermal titration calorimetry. The ligands differ only by a terminal carboxylate and/or methyl group. A surprisin ...

    The binding of four congeneric peptide-like thermolysin inhibitors has been studied by high-resolution crystal structure analysis and isothermal titration calorimetry. The ligands differ only by a terminal carboxylate and/or methyl group. A surprising non-additivity of functional group contributions for the carboxylate and/or methyl groups is detected. Adding the methyl first and then the carboxylate group results in a small Gibbs free energy increase and minor enthalpy/entropy partitioning for the first modification, whereas the second involves a strong affinity increase combined with large enthalpy/entropy changes. However, first adding the carboxylate and then the methyl group yields reverse effects: the acidic group attachment now causes minor effects, whereas the added methyl group provokes large changes. As all crystal structures show virtually identical binding modes, affinity changes are related to rearrangements of the first solvation layer next to the S(2)' pocket. About 20-25 water molecules are visible next to the studied complexes. The added COO(-) groups perturb the local water network in both carboxylated complexes, and the attached methyl groups provide favorable interaction sites for water molecules. Apart from one example, a contiguously connected water network between protein and ligand functional groups is observed in all complexes. In the complex with the carboxylated ligand, which still lacks the terminal methyl group, the water network is unfavorably ruptured. This results in a surprising thermodynamic signature showing only a minor affinity increase upon COO(-) group attachment. Because the further added methyl group provides a favorable interaction site for water, the network can be reestablished, and a strong affinity increase with a large enthalpy/entropy signature is then detected.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermolysin
A
316Bacillus thermoproteolyticusGene Names: npr
EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
UBX
Query on UBX

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Download CCD File 
A
N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-methyl-L-leucinamide
C16 H26 N3 O5 P
VZBGTFZRCJNJEQ-AWEZNQCLSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000980 (UBX)
Query on PRD_000980
AN-[(S)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-METHYL-L-LEUCINAMIDEPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.143 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.700α = 90.00
b = 92.700β = 90.00
c = 130.100γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
MAR345dtbdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-01
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Other
  • Version 1.2: 2014-02-12
    Type: Database references