5MOQ

Joint X-ray/neutron structure of cationic trypsin in complex with benzamidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.93 Å
  • R-Value Free: 0.103 
  • R-Value Work: 0.096 
  • R-Value Observed: 0.096 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report


This is version 2.0 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:  
    5MNE, 5MNF, 5MNG, 5MNH, 5MNN, 5MNO, 5MNQ, 5MNZ, 5MO0, 5MO2, 5MOP, 5MOQ, 5MOS

  • 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 is extremely rare and similarly the important role of water during binding remains poorly understood ...

    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. klebe@mailer.uni-marburg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cationic trypsinA223Bos taurusMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEN
Query on BEN

Download Ideal Coordinates CCD File 
C [auth A]BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BAM BindingDB:  5MOQ Ki: min: 4800, max: 3.90e+4 (nM) from 3 assay(s)
-TΔS: min: -9.91e+0, max: -3.01e+0 (kJ/mol) from 4 assay(s)
ΔH: min: -2.37e+1, max: -1.70e+1 (kJ/mol) from 4 assay(s)
ΔG: min: -2.69e+1, max: -2.66e+1 (kJ/mol) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.93 Å
  • R-Value Free: 0.103 
  • R-Value Work: 0.096 
  • R-Value Observed: 0.096 
  • Space Group: P 21 21 21
  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.901α = 90
b = 58.614β = 90
c = 67.604γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
HKL-2000data reduction
XDSdata scaling
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council268145-DrugProfilBind

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-14
    Changes: Data collection
  • Version 2.0: 2021-08-04
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary