1HVS

STRUCTURAL BASIS OF DRUG RESISTANCE FOR THE V82A MUTANT OF HIV-1 PROTEASE: BACKBONE FLEXIBILITY AND SUBSITE REPACKING

• PDB DOI: https://doi.org/10.2210/pdb1HVS/pdb

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


• Deposited: 1994-11-17 Released: 1995-02-14 
• Deposition Author(s): Baldwin, E.T., Bhat, T.N., Liu, B., Pattabiraman, N., Erickson, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Work: 0.150 
• R-Value Observed: 0.150 

Literature

Structural basis of drug resistance for the V82A mutant of HIV-1 proteinase.

Baldwin, E.T., Bhat, T.N., Liu, B., Pattabiraman, N., Erickson, J.W.

(1995) Nat Struct Biol 2: 244-249

• PubMed: 7773792 
• DOI: https://doi.org/10.1038/nsb0395-244


• PubMed Abstract: 
  

  A major problem in the development of antiviral therapies for AIDS has been the emergence of drug resistance. We report an analysis of the structure of a Val 82 to Ala mutant of HIV-1 proteinase complexed to A-77003, a C2 symmetry-based inhibitor. Modelling studies predicted that the V82A mutation would result in decreased van der Waals' interactions with the phenyl rings of A-77003 in both S1 and S1' subsites. Unexpected rearrangements of the protein backbone, however, resulted in favourable re-packing of inhibitor and enzyme atoms in the S1 but not the S1' subsite. This analysis reveals the importance of enzyme flexibility in accommodating alternate packing arrangements, and can be applied to the re-design of inhibitors targeted to drug resistant variants which emerge in the clinic.

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Organizational Affiliation: 

Frederick Biomedical Supercomputing Center, PRI/DynCorp, National Cancer Institute-Frederick Cancer Research and Development Center, Maryland 21702-1201, USA.

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: 22.35 kDa 
• Atom Count: 1,570 
• Modelled 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	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B (isolate BH5)) Explore P04587  Go to UniProtKB:  P04587

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A77	C [auth A]	N-{1-BENZYL-(2R,3S)-2,3-DIHYDROXY-4-[3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRYLAMINO]-5-PHENYL-PENTYL}-3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRAMIDE C44 H58 N8 O6 QPVWMQXBTCSLCB-BYAJYZPISA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
A77	PDBBind:  1HVS	Ki: 0.05 (nM) from 1 assay(s)
	Binding MOAD:  1HVS	Ki: 0.05 (nM) from 1 assay(s)
	BindingDB:  1HVS	Ki: 0.01 (nM) from 1 assay(s)
		Kd: 0.08 (nM) from 1 assay(s)
		IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Work: 0.150 
• R-Value Observed: 0.150 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.9	α = 90
b = 59.6	β = 90
c = 62.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-02-14 
Deposition Author(s): Baldwin, E.T., Bhat, T.N., Liu, B., Pattabiraman, N., Erickson, J.W.

Revision History  

• Version 1.0: 1995-02-14
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other