8FXQ | pdb_00008fxq

The Crystal Sturucture of Rhizopuspepsin with a bound modified peptide inhibitor generated by de novo drug design.

• PDB DOI: https://doi.org/10.2210/pdb8FXQ/pdb

• Classification: HYDROLASE
• Organism(s): Rhizopus microsporus var. chinensis, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-01-25 Released: 2023-02-08 
• Deposition Author(s): Satyshur, K.A., Rich, D.H., Ripka, A.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Aspartic protease inhibitors designed from computer-generated templates bind as predicted.

Ripka, A.S., Satyshur, K.A., Bohacek, R.S., Rich, D.H.

(2001) Org Lett 3: 2309-2312

• PubMed: 11463303 
• DOI: https://doi.org/10.1021/ol016090+
• Primary Citation Related Structures: 
  8FXQ


• PubMed Abstract: 
  

  [reaction: see text] Novel tripeptide-derived peptidomimetics 1, 7ab, and 8ab, inspired by templates generated by the structure-generating program GrowMol, were synthesized, shown to inhibit Rhizopus chinensis pepsin, and found by X-ray crystallography to bind to the enzyme in the GrowMol-predicted mode. Repetitive evaluation of the computer-generated templates for synthetic feasibility and optimal enzyme interactions led to the designed compounds.

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Organizational Affiliation: 
• School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.4 kDa 
• Atom Count: 5,735 
• Modeled Residue Count: 661 
• Deposited Residue Count: 666 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhizopuspepsin	A, B	329	Rhizopus microsporus var. chinensis	Mutation(s): 3  EC: 3.4.23.21
UniProt
Find proteins for P06026 (Rhizopus chinensis) Explore P06026  Go to UniProtKB:  P06026

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-CYS-VAL-LYS	C [auth W], D [auth Y]	4	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CHX (Subject of Investigation/LOI)	F [auth W], G [auth Y]	CYCLOHEXANE C6 H12 XDTMQSROBMDMFD-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/989

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.873	α = 90
b = 71.696	β = 90
c = 120.736	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-08 
Deposition Author(s): Satyshur, K.A., Rich, D.H., Ripka, A.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM50113

Revision History  

• Version 1.0: 2023-02-08
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Structure summary