1ZPK

Crystal structure of the complex of mutant HIV-1 protease (A71V, V82T, I84V) with a hydroxyethylamine peptidomimetic inhibitor BOC-PHE-PSI[R-CH(OH)CH2NH]-PHE-GLU-PHE-NH2

• PDB DOI: https://doi.org/10.2210/pdb1ZPK/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-05-17 Released: 2006-04-25 
• Deposition Author(s): Duskova, J., Skalova, T., Dohnalek, J., Petrokova, H., Hasek, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.253 
• R-Value Work: 0.156 
• R-Value Observed: 0.159 

Starting Model: experimental

Literature

Mutational Study of Pseudopeptide Inhibitor Binding to HIV-1 Protease; Analysis of Four X-ray Structures

Duskova, J., Skalova, T., Dohnalek, J., Petrokova, H., Hasek, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 22.55 kDa 
• Atom Count: 1,856 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASE RETROPEPSIN	A, B	99	Human immunodeficiency virus 1	Mutation(s): 3  EC: 3.4.23.16
UniProt
Find proteins for Q7ZCL6 (Human immunodeficiency virus 1) Explore Q7ZCL6  Go to UniProtKB:  Q7ZCL6
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Go to UniProtKB:  P03367

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0ZS	C [auth A]	N-{(2R,3S)-3-[(tert-butoxycarbonyl)amino]-2-hydroxy-4-phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl-L-phenylalaninamide C38 H49 N5 O8 MPMUDVMRFYJRLP-QEUNAIBPSA-N
CL	D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000385 (0ZS)	C [auth A]	BOC-PHE-PSI[R-CH(OH)CH2NH]-PHE-GLU-PHE-NH2	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.253 
• R-Value Work: 0.156 
• R-Value Observed: 0.159 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.483	α = 90
b = 62.483	β = 90
c = 82.412	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-25 
Deposition Author(s): Duskova, J., Skalova, T., Dohnalek, J., Petrokova, H., Hasek, J.

Revision History  

• Version 1.0: 2006-04-25
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-23
  Changes: Data collection, Refinement description
• Version 1.6: 2024-11-06
  Changes: Structure summary