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- PDB-8vb1: Crystal structure of HIV-1 protease with GS-9770 -

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Basic information

Entry
Database: PDB / ID: 8vb1
TitleCrystal structure of HIV-1 protease with GS-9770
ComponentsHIV-1 protease
KeywordsVIRAL PROTEIN / HIV / protease / antiviral / inhibitor
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Biological speciesHIV-1 06TG.HT043 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsLansdon, E.B.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Antimicrob.Agents Chemother. / Year: 2024
Title: Preclinical characterization of a non-peptidomimetic HIV protease inhibitor with improved metabolic stability.
Authors: Mulato, A. / Lansdon, E. / Aoyama, R. / Voigt, J. / Lee, M. / Liclican, A. / Lee, G. / Singer, E. / Stafford, B. / Gong, R. / Murray, B. / Chan, J. / Lee, J. / Xu, Y. / Ahmadyar, S. / ...Authors: Mulato, A. / Lansdon, E. / Aoyama, R. / Voigt, J. / Lee, M. / Liclican, A. / Lee, G. / Singer, E. / Stafford, B. / Gong, R. / Murray, B. / Chan, J. / Lee, J. / Xu, Y. / Ahmadyar, S. / Gonzalez, A. / Cho, A. / Stepan, G.J. / Schmitz, U. / Schultz, B. / Marchand, B. / Brumshtein, B. / Wang, R. / Yu, H. / Cihlar, T. / Xu, L. / Yant, S.R.
History
DepositionDec 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 protease
B: HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4753
Polymers21,6642
Non-polymers8111
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-26 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.493, 57.037, 85.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein HIV-1 protease / / Pol protein


Mass: 10831.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 06TG.HT043 (virus) / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: G0X8E8
#2: Chemical ChemComp-A1AAD / (2S)-2-{(3M)-4-chloro-3-[1-(difluoromethyl)-1H-1,2,4-triazol-5-yl]phenyl}-2-[(2E,4R)-4-[4-(2-cyclopropyl-2H-1,2,3-triazol-4-yl)phenyl]-2-imino-5-oxo-4-(3,3,3-trifluoro-2,2-dimethylpropyl)imidazolidin-1-yl]ethyl [1-(difluoromethyl)cyclopropyl]carbamate


Mass: 811.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H34ClF7N10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 2.25M ammonium acetate 100mM MES pH 6.5

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Data collection

DiffractionMean temperature: 170 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→47.5 Å / Num. obs: 54560 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 12.65 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.8
Reflection shellResolution: 1.3→1.38 Å / Num. unique obs: 4483 / CC1/2: 0.722

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→47.47 Å / SU ML: 0.1518 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 22.1071
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2192 2000 3.67 %
Rwork0.1998 52560 -
obs0.2005 54560 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.22 Å2
Refinement stepCycle: LAST / Resolution: 1.3→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 56 267 1843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821626
X-RAY DIFFRACTIONf_angle_d0.98962220
X-RAY DIFFRACTIONf_chiral_restr0.0851259
X-RAY DIFFRACTIONf_plane_restr0.0084271
X-RAY DIFFRACTIONf_dihedral_angle_d20.4293227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.340.36391210.31433193X-RAY DIFFRACTION83.54
1.34-1.370.29611350.28013529X-RAY DIFFRACTION92.06
1.37-1.410.25351380.24263618X-RAY DIFFRACTION94.16
1.41-1.460.2461400.22493688X-RAY DIFFRACTION96.11
1.46-1.510.25181400.21753702X-RAY DIFFRACTION96.58
1.51-1.570.19891420.20633730X-RAY DIFFRACTION97.14
1.57-1.640.24871440.20653775X-RAY DIFFRACTION98.07
1.64-1.730.23091450.19533804X-RAY DIFFRACTION98.38
1.73-1.840.22221460.19513830X-RAY DIFFRACTION98.93
1.84-1.980.19491470.19193853X-RAY DIFFRACTION99.21
1.98-2.180.20681470.19063863X-RAY DIFFRACTION99.43
2.18-2.490.21231480.19123897X-RAY DIFFRACTION99.63
2.49-3.140.24131510.20153963X-RAY DIFFRACTION99.73
3.14-47.470.19091560.18494115X-RAY DIFFRACTION99.6

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