6XCZ | pdb_00006xcz

Porcine pepsin in complex with saquinavir

• PDB DOI: https://doi.org/10.2210/pdb6XCZ/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2020-06-09 Released: 2021-06-16 
• Deposition Author(s): Vuksanovic, N., Silvaggi, N.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Porcine pepsin in complex with saquinavir

Vuksanovic, N., Silvaggi, N.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.26 kDa 
• Atom Count: 2,665 
• Modeled Residue Count: 326 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pepsin A	A	326	Sus scrofa	Mutation(s): 0  EC: 3.4.23.1
UniProt
Find proteins for P00791 (Sus scrofa) Explore P00791  Go to UniProtKB:  P00791

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ROC (Subject of Investigation/LOI)	B [auth A]	(2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide C38 H50 N6 O5 QWAXKHKRTORLEM-UGJKXSETSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000454 (ROC)	B [auth A]	Saquinavir	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.220 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.39	α = 90
b = 66.39	β = 90
c = 284.572	γ = 120

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-16 
Deposition Author(s): Vuksanovic, N., Silvaggi, N.R.

Revision History  

• Version 1.0: 2021-06-16
  Type: Initial release
  
• Version 1.1: 2021-08-18
  Changes: Data collection, Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary