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- PDB-8esx: HIV protease in complex with benzoxaborolone analog of darunavir -

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Basic information

Entry
Database: PDB / ID: 8esx
TitleHIV protease in complex with benzoxaborolone analog of darunavir
ComponentsProtease
KeywordsHYDROLASE/INHIBITOR / virus / protease / inhibitor / boron / HYDROLASE / HYDROLASE-INHIBITOR complex
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
ACETATE ION / Chem-X7B / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsWindsor, I.W. / Graham, B.J. / Raines, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM044783 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Inhibition of HIV-1 Protease by a Boronic Acid with High Oxidative Stability.
Authors: Graham, B.J. / Windsor, I.W. / Raines, R.T.
History
DepositionOct 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3819
Polymers21,4812
Non-polymers9007
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-59 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.970, 86.310, 45.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protease


Mass: 10740.677 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q5RZ08

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Non-polymers , 6 types, 220 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-X7B / [(3~{a}~{S},4~{R},6~{a}~{R})-2,3,3~{a},4,5,6~{a}-hexahydrofuro[2,3-b]furan-4-yl] ~{N}-[(2~{S},3~{R})-4-[[7,7-bis(oxidanyl)-9-oxidanylidene-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-3-yl]sulfonyl-(2-methylpropyl)amino]-3-oxidanyl-1-phenyl-butan-2-yl]carbamate


Mass: 619.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H36BN2O11S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris pH 7.5 and 500 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.35→48.1 Å / Num. obs: 50793 / % possible obs: 98.8 % / Redundancy: 11.8 % / Biso Wilson estimate: 17.61 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.076 / Net I/σ(I): 18.23
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3576 / CC1/2: 0.473 / Rrim(I) all: 2.263 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6c8x

6c8x


Resolution: 1.35→48.1 Å / SU ML: 0.1708 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2058 2000 3.94 %
Rwork0.1831 48793 -
obs0.184 50793 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.86 Å2
Refinement stepCycle: LAST / Resolution: 1.35→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 57 213 1782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771658
X-RAY DIFFRACTIONf_angle_d1.17172267
X-RAY DIFFRACTIONf_chiral_restr0.0868270
X-RAY DIFFRACTIONf_plane_restr0.0068279
X-RAY DIFFRACTIONf_dihedral_angle_d18.2717244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.34771360.34823295X-RAY DIFFRACTION95.41
1.38-1.420.30121380.28743398X-RAY DIFFRACTION97.87
1.42-1.460.29961400.25633418X-RAY DIFFRACTION98.1
1.46-1.510.25511410.24443417X-RAY DIFFRACTION98.34
1.51-1.560.27421390.23583413X-RAY DIFFRACTION98.15
1.56-1.630.25441430.2263465X-RAY DIFFRACTION98.85
1.63-1.70.20991410.19363463X-RAY DIFFRACTION98.85
1.7-1.790.24261420.18523461X-RAY DIFFRACTION99.28
1.79-1.90.2041440.17563516X-RAY DIFFRACTION99.35
1.9-2.050.18011440.17383496X-RAY DIFFRACTION99.59
2.05-2.260.19071440.16693516X-RAY DIFFRACTION99.78
2.26-2.580.1921460.18253574X-RAY DIFFRACTION100
2.58-3.250.17761480.17483601X-RAY DIFFRACTION100
3.25-48.10.21540.16433760X-RAY DIFFRACTION99.95

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