5MO0

Neutron structure of cationic trypsin in complex with benzamidine

Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.502 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes.

Schiebel, J., Gaspari, R., Wulsdorf, T., Ngo, K., Sohn, C., Schrader, T.E., Cavalli, A., Ostermann, A., Heine, A., Klebe, G.

(2018) Nat Commun 9: 3559-3559

  • DOI: 10.1038/s41467-018-05769-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Hydrogen bonds are key interactions determining protein-ligand binding affinity and therefore fundamental to any biological process. Unfortunately, explicit structural information about hydrogen positions and thus H-bonds in protein-ligand complexes ...

    Hydrogen bonds are key interactions determining protein-ligand binding affinity and therefore fundamental to any biological process. Unfortunately, explicit structural information about hydrogen positions and thus H-bonds in protein-ligand complexes is extremely rare and similarly the important role of water during binding remains poorly understood. Here, we report on neutron structures of trypsin determined at very high resolutions ≤1.5 Å in uncomplexed and inhibited state complemented by X-ray and thermodynamic data and computer simulations. Our structures show the precise geometry of H-bonds between protein and the inhibitors N-amidinopiperidine and benzamidine along with the dynamics of the residual solvation pattern. Prior to binding, the ligand-free binding pocket is occupied by water molecules characterized by a paucity of H-bonds and high mobility resulting in an imperfect hydration of the critical residue Asp189. This phenomenon likely constitutes a key factor fueling ligand binding via water displacement and helps improving our current view on water influencing protein-ligand recognition.

    Organizational Affiliation: 

    Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cationic trypsin
A
223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BAM
Query on BAM
Download SDF File 
Download CCD File 
A
BENZAMIDINE
C7 H9 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-O
 Ligand Interaction
DOD
Query on DOD
Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.502 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.147 
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council268145-DrugProfilBind268145-DrugProfilBind

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-09-12
    Type: Data collection, Database references
  • Version 1.2: 2018-11-14
    Type: Data collection