5VJ3

HIV Protease (PR) in open form with Mg2+ in active site and HIVE-9 in eye site

• PDB DOI: https://doi.org/10.2210/pdb5VJ3/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-18 Released: 2018-04-18 
• Deposition Author(s): Tiefenbrunn, T., Stout, C.D.
• 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: 2.00 Å
• R-Value Free: 0.279 
• R-Value Work: 0.219 
• R-Value Observed: 0.222 

Literature

Fragment-based campaign for the identification of potential exosite binders of HIV-1 Protease

Forli, S., Tiefenbrunn, T., Baksh, M.M., Chang, M.W., Perryman, A., Garg, D., Happer, M., Lin, Y.-C., Goodsell, D., Angelina, E.L., De Vera, I., Kojetin, D., Torbett, B.E., Finn, M.G., Elder, J., Stout, C.D., Olson, A.

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: 11.24 kDa 
• Atom Count: 824 
• Modelled Residue Count: 99 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A	99	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: pol EC: 3.4.23.16
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HV9	B [auth A]	4-methyl-N-({1-[4-(trifluoromethyl)pyrimidin-2-yl]piperidin-4-yl}carbamoyl)benzene-1-sulfonamide C18 H20 F3 N5 O3 S YEGSVKBKIFWARL-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.279 
• R-Value Work: 0.219 
• R-Value Observed: 0.222 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.925	α = 90
b = 48.925	β = 90
c = 103.012	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-04-18 
Deposition Author(s): Tiefenbrunn, T., Stout, C.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1P50GM103368

Revision History  

• Version 1.0: 2018-04-18
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description