Macromolecule Content

Total Structure Weight: 22.22 kDa
Atom Count: 1864
Residue Count: 198
Unique protein chains: 1

3D1Y

Crystal structure of HIV-1 mutant I54V and inhibitor SAQUINA

DOI: 10.2210/pdb3D1Y/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Human immunodeficiency virus type 1 (BH5 ISOLATE)
Mutation(s): Yes

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

Experimental Data Snapshot

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

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: 10.1016/j.jmb.2008.05.062
Structures With Same Primary Citation

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.

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

Organizational Affiliation:

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

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
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)
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B (isolate BH5)) Go to UniProtKB: P04587
Protein Feature View Full Protein Feature View for P04587

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ROC Query on ROC Download CCD File	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		Ligand Interaction
CL Query on CL Download CCD File	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction
NA Query on NA Download CCD File	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000454 (ROC) Query on PRD_000454	A	Saquinavir	Peptide-like / Inhibitor		--

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ROC	ΔH: 31.770000457763672 kJ/mol BindingDB
ROC	ΔG: 55.59000015258789 kJ/mol BindingDB
ROC	ΔH: 10.869999885559082 kJ/mol BindingDB
ROC	Ki: 0.8999999761581421 nM BindingDB
ROC	ΔG: 54.34000015258789 kJ/mol BindingDB
ROC	Ki: 1.0299999713897705 nM BindingDB
ROC	ΔG: 59.77000045776367 kJ/mol BindingDB
ROC	-TΔS: 33.040000915527344 kJ/mol BindingDB
ROC	Ki: 0.23000000417232513 nM BindingDB
ROC	ΔH: 35.529998779296875 kJ/mol BindingDB
ROC	ΔG: 43.470001220703125 kJ/mol BindingDB
ROC	Ki: 15 nM BindingDB
ROC	IC50: 11 nM BindingDB
ROC	ΔH: 43.470001220703125 kJ/mol BindingDB
ROC	ΔH: 16.299999237060547 kJ/mol BindingDB
ROC	Ki: 6 nM PDBBind
ROC	Ki: 0.44999998807907104 nM BindingDB
ROC	-TΔS: 35.119998931884766 kJ/mol BindingDB
ROC	IC50: 0.4000000059604645 nM BindingDB
ROC	-TΔS: 61.47999954223633 kJ/mol BindingDB
ROC	ΔH: 8.779999732971191 kJ/mol BindingDB
ROC	ΔH: 14.630000114440918 kJ/mol BindingDB
ROC	ΔH: 6.690000057220459 kJ/mol BindingDB
ROC	-TΔS: 65.23999786376953 kJ/mol BindingDB
ROC	ΔH: 17.969999313354492 kJ/mol BindingDB
ROC	IC50: 1.7999999523162842 nM BindingDB
ROC	ΔH: 22.56999969482422 kJ/mol BindingDB
ROC	ΔH: 7.940000057220459 kJ/mol BindingDB
ROC	ΔG: 49.7400016784668 kJ/mol BindingDB
ROC	IC50: 45 nM BindingDB
ROC	ΔG: 36.779998779296875 kJ/mol BindingDB
ROC	ΔG: 40.130001068115234 kJ/mol BindingDB
ROC	ΔH: 20.059999465942383 kJ/mol BindingDB
ROC	-TΔS: 66.48999786376953 kJ/mol BindingDB
ROC	IC50: 30 nM BindingDB
ROC	ΔH: 30.93000030517578 kJ/mol BindingDB
ROC	ΔH: 18.389999389648438 kJ/mol BindingDB
ROC	Ki: 2 nM BindingDB
ROC	ΔH: 0.07999999821186066 kJ/mol BindingDB
ROC	Ki: 0.07000000029802322 nM BindingDB
ROC	ΔG: 60.61000061035156 kJ/mol BindingDB
ROC	-TΔS: 59.810001373291016 kJ/mol BindingDB
ROC	Ki: 117 nM BindingDB
ROC	ΔG: 43.470001220703125 kJ/mol BindingDB
ROC	-TΔS: 43.91999816894531 kJ/mol BindingDB
ROC	ΔH: 14.630000114440918 kJ/mol BindingDB
ROC	ΔG: 53.5 kJ/mol BindingDB
ROC	ΔG: 35.529998779296875 kJ/mol BindingDB
ROC	-TΔS: 80.29000091552734 kJ/mol BindingDB
ROC	ΔG: 47.650001525878906 kJ/mol BindingDB
ROC	IC50: 8.399999618530273 nM BindingDB
ROC	ΔH: 40.130001068115234 kJ/mol BindingDB
ROC	-TΔS: 60.22999954223633 kJ/mol BindingDB
ROC	ΔG: 57.68000030517578 kJ/mol BindingDB
ROC	-TΔS: 77.37000274658203 kJ/mol BindingDB
ROC	-TΔS: 65.6500015258789 kJ/mol BindingDB
ROC	ΔG: 60.61000061035156 kJ/mol BindingDB
ROC	-TΔS: 76.94999694824219 kJ/mol BindingDB
ROC	ΔH: 15.050000190734863 kJ/mol BindingDB
ROC	ΔH: 25.079999923706055 kJ/mol BindingDB
ROC	-TΔS: 64.81999969482422 kJ/mol BindingDB
ROC	ΔG: 42.63999938964844 kJ/mol BindingDB
ROC	ΔH: 15.470000267028809 kJ/mol BindingDB
ROC	-TΔS: 43.08000183105469 kJ/mol BindingDB
ROC	ΔG: 62.279998779296875 kJ/mol BindingDB
ROC	-TΔS: 28.030000686645508 kJ/mol BindingDB
ROC	ΔG: 53.5 kJ/mol BindingDB
ROC	ΔH: 9.199999809265137 kJ/mol BindingDB
ROC	ΔH: 40.130001068115234 kJ/mol BindingDB
ROC	IC50: 1 nM BindingDB
ROC	ΔH: 15.470000267028809 kJ/mol BindingDB
ROC	ΔG: 53.5 kJ/mol BindingDB
ROC	-TΔS: 79.04000091552734 kJ/mol BindingDB
ROC	-TΔS: 65.6500015258789 kJ/mol BindingDB
ROC	ΔG: 49.31999969482422 kJ/mol BindingDB
ROC	-TΔS: 55.630001068115234 kJ/mol BindingDB
ROC	ΔG: 61.45000076293945 kJ/mol BindingDB
ROC	-TΔS: 61.45000076293945 kJ/mol BindingDB
ROC	IC50: 16 nM BindingDB
ROC	ΔG: 44.310001373291016 kJ/mol BindingDB
ROC	ΔH: 12.539999961853027 kJ/mol BindingDB
ROC	ΔG: 52.66999816894531 kJ/mol BindingDB
ROC	ΔH: 12.119999885559082 kJ/mol BindingDB
ROC	ΔG: 49.31999969482422 kJ/mol BindingDB
ROC	-TΔS: 50.27000045776367 kJ/mol BindingDB
ROC	ΔG: 53.5 kJ/mol BindingDB
ROC	ΔG: 51 kJ/mol BindingDB
ROC	-TΔS: 65.23999786376953 kJ/mol BindingDB
ROC	Ki: 0.4300000071525574 nM BindingDB
ROC	ΔG: 41.79999923706055 kJ/mol BindingDB
ROC	-TΔS: 44.75 kJ/mol BindingDB
ROC	ΔH: 12.119999885559082 kJ/mol BindingDB
ROC	ΔH: 8.779999732971191 kJ/mol BindingDB
ROC	ΔG: 38.040000915527344 kJ/mol BindingDB
ROC	Ki: 0.03999999910593033 nM BindingDB
ROC	-TΔS: 46.41999816894531 kJ/mol BindingDB
ROC	ΔG: 56.43000030517578 kJ/mol BindingDB
ROC	ΔH: 10.029999732971191 kJ/mol BindingDB
ROC	-TΔS: 43.91999816894531 kJ/mol BindingDB
ROC	-TΔS: 64.81999969482422 kJ/mol BindingDB
ROC	Ki: 1.399999976158142 nM BindingDB
ROC	ΔG: 55.18000030517578 kJ/mol BindingDB
ROC	ΔH: 21.31999969482422 kJ/mol BindingDB
ROC	ΔH: 5.019999980926514 kJ/mol BindingDB
ROC	-TΔS: 46.84000015258789 kJ/mol BindingDB
ROC	Ki: 89.52999877929688 nM BindingDB
ROC	ΔG: 52.25 kJ/mol BindingDB
ROC	-TΔS: 57.29999923706055 kJ/mol BindingDB
ROC	-TΔS: 71.11000061035156 kJ/mol BindingDB
ROC	Kd: 0.3100000023841858 nM BindingDB
ROC	-TΔS: 58.59000015258789 kJ/mol BindingDB
ROC	ΔG: 54.7599983215332 kJ/mol BindingDB
ROC	ΔH: 13.789999961853027 kJ/mol BindingDB
ROC	-TΔS: 58.13999938964844 kJ/mol BindingDB
ROC	Ki: 48 nM BindingDB
ROC	Ki: 0.46000000834465027 nM BindingDB
ROC	-TΔS: 70.2699966430664 kJ/mol BindingDB
ROC	-TΔS: 30.530000686645508 kJ/mol BindingDB
ROC	Ki: 0.11999999731779099 nM BindingDB
ROC	IC50: 1.7000000476837158 nM BindingDB
ROC	Ki: 6 nM Binding MOAD
ROC	Kd: 0.3199999928474426 nM BindingDB
ROC	-TΔS: 56.86000061035156 kJ/mol BindingDB
ROC	Ki: 1.7999999523162842 nM BindingDB
ROC	ΔH: 25.5 kJ/mol BindingDB
ROC	ΔH: 12.960000038146973 kJ/mol BindingDB
ROC	Ki: 0.05999999865889549 nM BindingDB
ROC	ΔH: 3.759999990463257 kJ/mol BindingDB
ROC	ΔH: 12.539999961853027 kJ/mol BindingDB
ROC	Ki: 0.1899999976158142 nM BindingDB
ROC	-TΔS: 71.5 kJ/mol BindingDB
ROC	-TΔS: 59.38999938964844 kJ/mol BindingDB
ROC	ΔG: 38.869998931884766 kJ/mol BindingDB
ROC	ΔG: 41.79999923706055 kJ/mol BindingDB
ROC	-TΔS: 57.33000183105469 kJ/mol BindingDB
ROC	Ki: 0.25 nM BindingDB
ROC	Ki: 78.44000244140625 nM BindingDB
ROC	IC50: 0.3400000035762787 nM BindingDB
ROC	-TΔS: 41 kJ/mol BindingDB
ROC	ΔH: 26.75 kJ/mol BindingDB
ROC	ΔH: 11.699999809265137 kJ/mol BindingDB
ROC	ΔG: 57.27000045776367 kJ/mol BindingDB
ROC	ΔH: 8.359999656677246 kJ/mol BindingDB
ROC	-TΔS: 75.27999877929688 kJ/mol BindingDB
ROC	-TΔS: 74.02999877929688 kJ/mol BindingDB
ROC	-TΔS: 61.900001525878906 kJ/mol BindingDB
ROC	Ki: 3.700000047683716 nM BindingDB
ROC	ΔH: 27.59000015258789 kJ/mol BindingDB
ROC	ΔG: 51.40999984741211 kJ/mol BindingDB
ROC	ΔH: 11.699999809265137 kJ/mol BindingDB
ROC	ΔG: 50.15999984741211 kJ/mol BindingDB
ROC	-TΔS: 30.110000610351562 kJ/mol BindingDB
ROC	-TΔS: 60.63999938964844 kJ/mol BindingDB
ROC	ΔG: 53.09000015258789 kJ/mol BindingDB
ROC	ΔH: 9.199999809265137 kJ/mol BindingDB
ROC	IC50: 0.20000000298023224 nM BindingDB
ROC	ΔG: 60.189998626708984 kJ/mol BindingDB
ROC	-TΔS: 61.900001525878906 kJ/mol BindingDB
ROC	Ki: 1.2999999523162842 nM BindingDB
ROC	ΔG: 47.22999954223633 kJ/mol BindingDB
ROC	IC50: 270 nM BindingDB
ROC	ΔG: 45.97999954223633 kJ/mol BindingDB
ROC	ΔG: 47.22999954223633 kJ/mol BindingDB
ROC	IC50: 11.199999809265137 nM BindingDB
ROC	ΔH: 9.609999656677246 kJ/mol BindingDB
ROC	IC50: 0.23000000417232513 nM BindingDB
ROC	ΔH: 2.0899999141693115 kJ/mol BindingDB
ROC	-TΔS: 33.040000915527344 kJ/mol BindingDB
ROC	Ki: 0.5199999809265137 nM BindingDB
ROC	IC50: 0.4000000059604645 nM BindingDB
ROC	ΔG: 51.83000183105469 kJ/mol BindingDB
ROC	ΔG: 50.58000183105469 kJ/mol BindingDB
ROC	ΔG: 50.15999984741211 kJ/mol BindingDB
ROC	ΔH: 35.11000061035156 kJ/mol BindingDB

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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2008-05-06
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

Prepare Data

Validate Data

Deposit Data

Deposition Help & Resources

164391 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education