4GB2 | pdb_00004gb2

HIV-1 protease (mutant Q7K L33I L63I) in complex with a bicyclic pyrrolidine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4GB2/pdb

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


• Deposited: 2012-07-26 Released: 2013-07-31 
• Deposition Author(s): Stieler, M., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Cocrystallization of potent pyrrolidine based HIV-1 protease inhibitors

Stieler, M., Klee, N., Heine, A., Doerr, S., Diederich, W., Klebe, G.

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: 22.39 kDa 
• Atom Count: 1,780 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag-Pol polyprotein	A, B	99	Human immunodeficiency virus type 1 (BRU ISOLATE)	Mutation(s): 3  Gene Names: gag-pol EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.1.13.2 (PDB Primary Data)
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367  Go to UniProtKB:  P03367

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0LQ	F [auth B]	(4aS,7aS)-1,4-bis(diphenylmethyl)hexahydro-1H-pyrrolo[3,4-b]pyrazine-2,3-dione C32 H29 N3 O2 YLCOBFHUORVRLI-NSOVKSMOSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], G [auth B], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.661	α = 90
b = 86.637	β = 90
c = 45.892	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-31 
Deposition Author(s): Stieler, M., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2013-07-31
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description