Biological Assembly 1  

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: 22.22 kDa 
• Atom Count: 1,864 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

 3D1Y

Crystal structure of HIV-1 mutant I54V and inhibitor SAQUINA

• PDB DOI: 10.2210/pdb3D1Y/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 (BH5 ISOLATE)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-05-06 Released: 2008-05-27 
• Deposition Author(s): Liu, F., Weber, I.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.174 
• R-Value Work: 0.150 

Literature

Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir.

Liu, F., Kovalevsky, A.Y., Tie, Y., Ghosh, A.K., Harrison, R.W., Weber, I.T.

(2008) J Mol Biol 381: 102-115

• PubMed: 18597780 
• DOI: 10.1016/j.jmb.2008.05.062
• Primary Citation of Related Structures:  
  3CYW, 3CYX, 3D1X, 3D1Y, 3D1Z, 3D20


• PubMed Abstract: 
  

HIV-1 (human immunodeficiency virus type 1) protease (PR) and its mutants are important antiviral drug targets. The PR flap region is critical for binding substrates or inhibitors and catalytic activity. Hence, mutations of flap residues frequently contribute to reduced susceptibility to PR inhibitors in drug-resistant HIV. Structural and kinetic analyses were used to investigate the role of flap residues Gly48, Ile50, and Ile54 in the development of drug resistance. The crystal structures of flap mutants PR(I50V) (PR with I50V mutation), PR(I54V) (PR with I54V mutation), and PR(I54M) (PR with I54M mutation) complexed with saquinavir (SQV) as well as PR(G48V) (PR with G48V mutation), PR(I54V), and PR(I54M) complexed with darunavir (DRV) were determined at resolutions of 1.05-1.40 A. The PR mutants showed changes in flap conformation, interactions with adjacent residues, inhibitor binding, and the conformation of the 80s loop relative to the wild-type PR. The PR contacts with DRV were closer in PR(G48V)-DRV than in the wild-type PR-DRV, whereas they were longer in PR(I54M)-DRV. The relative inhibition of PR(I54V) and that of PR(I54M) were similar for SQV and DRV. PR(G48V) was about twofold less susceptible to SQV than to DRV, whereas the opposite was observed for PR(I50V). The observed inhibition was in agreement with the association of G48V and I50V with clinical resistance to SQV and DRV, respectively. This analysis of structural and kinetic effects of the mutants will assist in the development of more effective inhibitors for drug-resistant HIV.

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Related Citations: 

• Ultra-High Resolution Crystal Structure of HIV-1 Protease Mutant Reveals Two Binding Sites for Clinical Inhibitor Tmc114
  Kovalevsky, A.Y., Liu, F., Leshchenko, S., Ghosh, A.K., Harrison, R.W., Weber, I.T.
  (2006) J Mol Biol 365: 901

• Kinetic, Stability, and Structural Changes in High-Resolution Crystal Structures of HIV-1 Protease with Drug-Resistant Mutations L24I, I50V, and G73S.
  Liu, F., Boross, P.I., Wang, Y.F., Tozser, J., Louis, J.M., Harrison, R.W., Weber, I.T.
  (2005) J Mol Biol 354: 789

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Organizational Affiliation: 

Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, GA 30303, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Protease	A, B	99	Human immunodeficiency virus type 1 (BH5 ISOLATE)	Mutation(s): 1  Gene Names: gag-pol EC: 3.4.23.16 (PDB Primary Data), 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 P04587 (Human immunodeficiency virus type 1 group M subtype B (isolate BH5)) Explore P04587  Go to UniProtKB:  P04587

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ROC	E [auth A]	(2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide C38 H50 N6 O5 QWAXKHKRTORLEM-UGJKXSETSA-N
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ROC	BindingDB:  3D1Y	Ki: min: 0.04, max: 138 (nM) from 28 assay(s)
		Kd: min: 0.31, max: 67 (nM) from 6 assay(s)
		IC50: min: 0.2, max: 270 (nM) from 16 assay(s)
		-TΔS: min: -8.03e+1, max: -2.80e+1 (kJ/mol) from 44 assay(s)
		ΔH: min: -3.18e+1, max: 43.47 (kJ/mol) from 45 assay(s)
		ΔG: min: -6.23e+1, max: -3.55e+1 (kJ/mol) from 44 assay(s)
	Binding MOAD:  3D1Y	Ki: 6 (nM) from 1 assay(s)
	PDBBind:  3D1Y	Ki: 6 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000454 (ROC)	E [auth A]	Saquinavir	Peptide-like / Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.174 
• R-Value Work: 0.150 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.72	α = 90
b = 85.94	β = 90
c = 46.38	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Liu, F., Weber, I.T.

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2013-02-27
  Changes: Other
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations, Structure summary