Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 22.21 kDa 
• Atom Count: 1763 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

4DQE

Crystal Structure of (G16C/L38C) HIV-1 Protease in Complex with DRV

• PDB DOI: 10.2210/pdb4DQE/pdb

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


• Deposited: 2012-02-15 Released: 2012-03-07 
• Deposition Author(s): Schiffer, C.A., Mittal, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.219 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 

Literature

Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease.

Mittal, S., Cai, Y., Nalam, M.N., Bolon, D.N., Schiffer, C.A.

(2012) J Am Chem Soc 134: 4163-4168

• PubMed: 22295904 
• DOI: 10.1021/ja2095766
• Primary Citation of Related Structures:  
  4DQB, 4DQC, 4DQE, 4DQF, 4DQG, 4DQH


• PubMed Abstract: 
  

Human immunodeficiency virus Type-1 (HIV-1) protease is crucial for viral maturation and infectivity. Studies of protease dynamics suggest that the rearrangement of the hydrophobic core is essential for enzyme activity. Many mutations in the hydrophobic core are also associated with drug resistance and may modulate the core flexibility. To test the role of flexibility in protease activity, pairs of cysteines were introduced at the interfaces of flexible regions remote from the active site. Disulfide bond formation was confirmed by crystal structures and by alkylation of free cysteines and mass spectrometry. Oxidized and reduced crystal structures of these variants show the overall structure of the protease is retained. However, cross-linking the cysteines led to drastic loss in enzyme activity, which was regained upon reducing the disulfide cross-links. Molecular dynamics simulations showed that altered dynamics propagated throughout the enzyme from the engineered disulfide. Thus, altered flexibility within the hydrophobic core can modulate HIV-1 protease activity, supporting the hypothesis that drug resistant mutations distal from the active site can alter the balance between substrate turnover and inhibitor binding by modulating enzyme activity.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartyl protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: gag-pol EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P12499 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34)) Explore P12499  Go to UniProtKB:  P12499

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
017	C [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
ACT	D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
017	BindingDB:  4DQE	Ki: min: 2.00e-4, max: 2 (nM) from 15 assay(s)
		Kd: 0.02 (nM) from 1 assay(s)
		IC50: min: 0.06, max: 370 (nM) from 10 assay(s)
		EC50: min: 0.25, max: 112 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.219 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.241	α = 90
b = 58.473	β = 90
c = 61.75	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-15 
• Released Date: 2012-03-07 
Deposition Author(s): Schiffer, C.A., Mittal, S.

Revision History  

• Version 1.0: 2012-03-07
  Type: Initial release
  
• Version 1.1: 2012-05-02
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description