5M5F

Thermolysin in complex with inhibitor and krypton


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.111 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1' Pocket of Thermolysin.

Krimmer, S.G.Cramer, J.Schiebel, J.Heine, A.Klebe, G.

(2017) J. Am. Chem. Soc. 139: 10419-10431

  • DOI: 10.1021/jacs.7b05028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We investigated the hydration state of the deep, well-accessible hydrophobic S1' specificity pocket of the metalloprotease thermolysin with purposefully designed ligands using high-resolution crystallography and isothermal titration calorimetry. The ...

    We investigated the hydration state of the deep, well-accessible hydrophobic S1' specificity pocket of the metalloprotease thermolysin with purposefully designed ligands using high-resolution crystallography and isothermal titration calorimetry. The S1' pocket is known to recognize selectively a very stringent set of aliphatic side chains such as valine, leucine, and isoleucine of putative substrates. We engineered a weak-binding ligand covering the active site of the protease without addressing the S1' pocket, thus transforming it into an enclosed cavity. Its sustained accessibility could be proved by accommodating noble gas atoms into the pocket in the crystalline state. The topology and electron content of the enclosed pocket with a volume of 141 Å3 were analyzed using an experimental MAD-phased electron density map that was calibrated to an absolute electron number scale, enabling access to the total electron content within the cavity. Our analysis indicates that the S1' pocket is virtually vacated, thus free of any water molecules. The thermodynamic signature of the reduction of the void within the pocket by growing aliphatic P1' substituents (H, Me, iPr, iBu) reveals a dramatic, enthalpy-dominated gain in free energy of binding resulting in a factor of 41 000 in Kd for the H-to-iBu transformation. Substituents placing polar decoy groups into the pocket to capture putatively present water molecules could not collect any evidence for a bound solvent molecule.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermolysin
E
316Bacillus thermoproteolyticusMutation(s): 0 
Gene Names: npr
EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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

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E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
KR
Query on KR

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E
KRYPTON
Kr
DNNSSWSSYDEUBZ-UHFFFAOYSA-N
 Ligand Interaction
7GR
Query on 7GR

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E
(2~{S})-4-methyl-2-[2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]ethanoylamino]pentanoic acid
C17 H26 N3 O7 P
MOYNPRDFZGMZHZ-AWEZNQCLSA-N
 Ligand Interaction
DMS
Query on DMS

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E
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.111 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.428α = 90.00
b = 92.428β = 90.00
c = 130.192γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany268145-DrugProfilBind

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release