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- PDB-6pu8: Room temperature X-ray structure of HIV-1 protease triple mutant ... -

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Basic information

Entry
Database: PDB / ID: 6pu8
TitleRoom temperature X-ray structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with tetrahedral intermediate of keto-darunavir
ComponentsHIV-1 protease
KeywordsHYDROLASE / HIV-1 protease / aspartic protease / tetrahedral intermediate inhibitor / homodimer
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis / identical protein binding
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKovalevsky, A. / Das, A.
CitationJournal: Acs Omega / Year: 2020
Title: Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design.
Authors: Kumar, M. / Mandal, K. / Blakeley, M.P. / Wymore, T. / Kent, S.B.H. / Louis, J.M. / Das, A. / Kovalevsky, A.
History
DepositionJul 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: HIV-1 protease
B: HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0733
Polymers21,5092
Non-polymers5641
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-22 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.631, 87.438, 46.429
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HIV-1 protease


Mass: 10754.703 Da / Num. of mol.: 2 / Mutation: V32I,I47V,V82I
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: Q7SSI0
#2: Chemical ChemComp-P3V / (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S)-4-{[(4-aminophenyl)sulfonyl](2-methylpropyl)amino}-3,3-dihydroxy-1-phenylbutan-2-yl]carbamate


Mass: 563.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H37N3O8S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES, 1.0 M NaCl, pH 6.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5406 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 22743 / % possible obs: 98 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 29.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2253 / % possible all: 99

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E5J

5e5j


Resolution: 1.8→20 Å / Num. parameters: 6699 / Num. restraintsaints: 6296 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1074 5 %RANDOM
Rwork0.1861 ---
all0.1903 21338 --
obs-19795 92.2 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1658.5
Refinement stepCycle: 1 / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 39 121 1674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0252
X-RAY DIFFRACTIONs_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.064
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.025
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.085
X-RAY DIFFRACTIONs_approx_iso_adps0

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