3KT2 | pdb_00003kt2

Crystal Structure of N88D mutant HIV-1 Protease

• PDB DOI: https://doi.org/10.2210/pdb3KT2/pdb

• Classification: HYDROLASE
• Organism(s): HIV-1 M:B_HXB2R
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-11-24 Released: 2010-02-16 
• Deposition Author(s): Bihani, S.C., Das, A., Prashar, V., Ferrer, J.L., Hosur, M.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Resistance mechanism revealed by crystal structures of unliganded nelfinavir-resistant HIV-1 protease non-active site mutants N88D and N88S.

Bihani, S.C., Das, A., Prashar, V., Ferrer, J.L., Hosur, M.V.

(2009) Biochem Biophys Res Commun 389: 295-300

• PubMed: 19720046 
• DOI: https://doi.org/10.1016/j.bbrc.2009.08.138
• Primary Citation Related Structures: 
  3KT2, 3KT5


• PubMed Abstract: 
  

  Nelfinavir is an inhibitor of HIV-1 protease, and is used for treatment of patients suffering from HIV/AIDS. However, treatment results in drug resistant mutations in HIV-1 protease. N88D and N88S are two such mutations which occur in the non-active site region of the enzyme. We have determined crystal structures of unliganded N88D and N88S mutants of HIV-1 protease to resolution of 1.65A and 1.8A, respectively. These structures refined against synchrotron data lead to R-factors of 0.1859 and 0.1780, respectively. While structural effects of N88D are very subtle, the mutation N88S has caused a significant conformational change in D30, an active site residue crucial for substrate and inhibitor binding.

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Organizational Affiliation: 
• Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 21.96 kDa 
• Atom Count: 1,884 
• Modeled Residue Count: 198 
• Deposited Residue Count: 203 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A	203	HIV-1 M:B_HXB2R	Mutation(s): 4  Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.05	α = 90
b = 62.05	β = 90
c = 83.7	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-16 
Deposition Author(s): Bihani, S.C., Das, A., Prashar, V., Ferrer, J.L., Hosur, M.V.

Revision History  

• Version 1.0: 2010-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-23
  Changes: Source and taxonomy
• Version 1.3: 2021-11-10
  Changes: Database references
• Version 1.4: 2024-05-29
  Changes: Data collection