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- PDB-7to6: HIV-1 wild type protease with GRL-01717A, with C-4 substituted cy... -

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Basic information

Entry
Database: PDB / ID: 7to6
TitleHIV-1 wild type protease with GRL-01717A, with C-4 substituted cyclohexane-fused bis-tetrahydrofuran (Chf-THF) derivatives as P2-ligand [diastereomer 2]
ComponentsProtease
KeywordsVIRAL PROTEIN/INHIBITOR / SPARTIC ACID PROTEASE / INHIBITORS / VIRAL PROTEIN / VIRAL PROTEIN-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-G77 / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.21 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)22,3778
Polymers21,4812
Non-polymers8956
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-58 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.732, 86.238, 45.961
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 , 5 types, 216 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-G77 / (1S,3aR,4R,6R,7aS)-octahydro-1,6-epoxy-2-benzofuran-4-yl [(2S,3R)-4-{[2-(cyclopropylamino)-1,3-benzothiazole-6-sulfonyl](2-methylpropyl)amino}-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]carbamate


Mass: 706.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40F2N4O7S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 1.3 M NaCl, 0.1 Acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.21→50 Å / Num. obs: 68335 / % possible obs: 95.3 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.028 / Rrim(I) all: 0.068 / Χ2: 1.001 / Net I/σ(I): 22.9
Reflection shellResolution: 1.21→1.25 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5048 / CC1/2: 0.858 / CC star: 0.961 / Rpim(I) all: 0.243 / Rrim(I) all: 0.546 / Χ2: 1.004 / % possible all: 71.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.31 Å33.37 Å
Translation5.31 Å33.37 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER4.064 Datablock id: mmcif_pdbx.dicphasing
SHELX2014refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NU3

3nu3


Resolution: 1.21→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1876 3447 5 %RANDOM
Rwork0.1573 ---
all0.1588 68301 --
obs0.1588 68301 95.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso max: 81.39 Å2 / Biso mean: 18.6258 Å2 / Biso min: 9 Å2
Refinement stepCycle: final / Resolution: 1.21→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 108 210 1830
Biso mean--13.67 26.24 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.005
X-RAY DIFFRACTIONs_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.385
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.025
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
X-RAY DIFFRACTIONs_approx_iso_adps0.101

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