3OY4 | pdb_00003oy4

Crystal Structure of HIV-1 L76V Protease in Complex with the Protease Inhibitor Darunavir.

• PDB DOI: https://doi.org/10.2210/pdb3OY4/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): HIV-1 M:B_ARV2/SF2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-09-22 Released: 2011-02-09 
• Deposition Author(s): Schiffer, C.A., Nalivaika, E.A., Bandaranayake, R.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.219 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.178 (Depositor) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Crystal Structure of HIV-1 L76V Protease in Complex with the Protease Inhibitor Darunavir.

Schiffer, C.A., Nalivaika, E.A., Bandaranayake, R.M.

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: 22.94 kDa 
• Atom Count: 1,709 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 PROTEASE	A, B	99	HIV-1 M:B_ARV2/SF2	Mutation(s): 2  Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)) Explore P03369  Go to UniProtKB:  P03369

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
017	N [auth B]	(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE C27 H37 N3 O7 S CJBJHOAVZSMMDJ-HEXNFIEUSA-N
PO4	C [auth A], D [auth A], H [auth B], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.219 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.178 (Depositor) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.719	α = 90
b = 57.714	β = 90
c = 62.03	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-09 
Deposition Author(s): Schiffer, C.A., Nalivaika, E.A., Bandaranayake, R.M.

Revision History  

• Version 1.0: 2011-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations, Structure summary