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- PDB-7myp: Crystal Structure of HIV-1 PRS17 with GRL-44-10A -

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Basic information

Entry
Database: PDB / ID: 7myp
TitleCrystal Structure of HIV-1 PRS17 with GRL-44-10A
ComponentsProtease
KeywordsHYDROLASE/Inhibitor / HIV-1 Protease / Multi drug resistant / HYDROLASE-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
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAgniswamy, J. / Weber, I.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)AI150461 United States
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Novel HIV PR inhibitors with C4-substituted bis-THF and bis-fluoro-benzyl target the two active site mutations of highly drug resistant mutant PR S17 .
Authors: Agniswamy, J. / Kneller, D.W. / Ghosh, A.K. / Weber, I.T.
History
DepositionMay 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)22,4337
Polymers21,5852
Non-polymers8485
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-43 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.943, 62.943, 82.720
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protease / Retropepsin


Mass: 10792.645 Da / Num. of mol.: 2
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: I7AJ09
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-G04 / (3R,3aS,4R,6aR)-4-methoxyhexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate


Mass: 592.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H40N2O9S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.15 M sodium chloride, 0.1 M sodium acetate at pH 5.5

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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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 21295 / % possible obs: 95.2 % / Redundancy: 4.4 % / CC1/2: 0.829 / Net I/σ(I): 20.99
Reflection shellResolution: 1.65→1.71 Å / Num. unique obs: 1555 / CC1/2: 0.829

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T2Z

5t2z


Resolution: 1.65→29.43 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.747 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1011 4.7 %RANDOM
Rwork0.1995 ---
obs0.202 20281 95.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.02 Å2 / Biso mean: 28.624 Å2 / Biso min: 14.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.16 Å20 Å2
2--0.33 Å2-0 Å2
3----1.06 Å2
Refinement stepCycle: final / Resolution: 1.65→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 96 97 1715
Biso mean--28.35 37.61 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131790
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171810
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.6472455
X-RAY DIFFRACTIONr_angle_other_deg1.2721.5754204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7895228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28221.88469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06515310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1721510
X-RAY DIFFRACTIONr_chiral_restr0.0780.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021964
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02342
LS refinement shellResolution: 1.651→1.694 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 56 -
Rwork0.261 1062 -
all-1118 -
obs--69.05 %

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