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- PDB-7to5: HIV-1 wild type protease with GRL-05816A, with C-4 substituted cy... -

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Basic information

Entry
Database: PDB / ID: 7to5
TitleHIV-1 wild type protease with GRL-05816A, with C-4 substituted cyclohexane-fused bis-tetrahydrofuran (Chf-THF) derivatives as P2-ligand [diastereomer 1]
ComponentsProtease
KeywordsANTIVIRAL PROTEIN/INHIBITOR / ASPARTIC ACID PROTEASE / HIV-1 PROTEASE / INHIBITORS / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


host multivesicular body / aspartic-type endopeptidase activity / virion membrane / 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
FORMIC ACID / Chem-G8R / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.13 Å
AuthorsWang, Y.-F. / Agniswamy, J. / Ghosh, A.K. / Weber, I.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150466 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150461 United States
CitationJournal: Chemmedchem / Year: 2022
Title: Design, Synthesis and X-Ray Structural Studies of Potent HIV-1 Protease Inhibitors Containing C-4 Substituted Tricyclic Hexahydro-Furofuran Derivatives as P2 Ligands.
Authors: Ghosh, A.K. / Kovela, S. / Sharma, A. / Shahabi, D. / Ghosh, A.K. / Hopkins, D.R. / Yadav, M. / Johnson, M.E. / Agniswamy, J. / Wang, Y.F. / Hattori, S.I. / Higashi-Kuwata, N. / Aoki, M. / ...Authors: Ghosh, A.K. / Kovela, S. / Sharma, A. / Shahabi, D. / Ghosh, A.K. / Hopkins, D.R. / Yadav, M. / Johnson, M.E. / Agniswamy, J. / Wang, Y.F. / Hattori, S.I. / Higashi-Kuwata, N. / Aoki, M. / Amano, M. / Weber, I.T. / Mitsuya, H.
History
DepositionJan 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 18, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 18, 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

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4209
Polymers21,4812
Non-polymers9387
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-60 kcal/mol
Surface area9670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.943, 86.138, 46.097
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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 / Plasmid: pJ414 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3) / References: UniProt: Q5RZ08

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Non-polymers , 6 types, 286 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-G8R / (1R,3aS,4S,6S,7aR)-octahydro-1,6-epoxy-2-benzofuran-4-yl [(2S,3R)-4-{[2-(cyclopropylamino)-1,3-benzothiazole-6-sulfonyl](2-methylpropyl)amino}-3-hydroxy-1-phenylbutan-2-yl]carbamate


Mass: 670.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H42N4O7S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.5 M NaCl, 0.1M Sodium Acetate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→50 Å / Num. obs: 80849 / % possible obs: 91.6 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.018 / Rrim(I) all: 0.063 / Χ2: 1 / Net I/σ(I): 24.5 / Num. measured all: 712602
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.13-1.173.40.4145300.8680.9640.2480.4821.00952.1
1.17-1.224.10.29864990.9310.1630.3410.99174.5
1.22-1.275.70.21781850.970.0970.2390.99393.7
1.27-1.346.50.17286160.9850.0710.1860.99498.4
1.34-1.4270.14686390.9910.0570.1571.00599
1.42-1.5380.11886330.9950.0420.1261.00998
1.53-1.6911.10.08687550.9980.0260.091.00299.6
1.69-1.9312.80.06788640.9980.0190.0691.003100
1.93-2.4312.70.05588880.9980.0160.057199.5
2.43-5012.40.05292400.9970.0150.0540.99799.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.33 Å36.31 Å
Translation5.33 Å36.31 Å

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Processing

Software
NameVersionClassification
HKL-2000719.2data reduction
HKL-2000719.2data scaling
PHASER4.064 Datablock id: mmcif_pdbx.dicphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NU3

3nu3


Resolution: 1.13→36.34 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.727 / SU ML: 0.015 / SU R Cruickshank DPI: 0.0287 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1422 3976 4.9 %RANDOM
Rwork0.1226 ---
obs0.1236 76823 91.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.87 Å2 / Biso mean: 12.164 Å2 / Biso min: 4.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å2-0 Å20 Å2
2---0.26 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 1.13→36.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 111 279 1902
Biso mean--8.69 22.6 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0132022
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172119
X-RAY DIFFRACTIONr_angle_refined_deg2.7011.7152804
X-RAY DIFFRACTIONr_angle_other_deg1.5241.6364940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7235278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19922.43678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99515381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6431511
X-RAY DIFFRACTIONr_chiral_restr0.9070.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022252
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02434
X-RAY DIFFRACTIONr_rigid_bond_restr4.86634141
LS refinement shellResolution: 1.131→1.16 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 159 -
Rwork0.34 2955 -
all-3114 -
obs--48.28 %

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