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- PDB-6ogt: X-ray crystal structure of darunavir-resistant HIV-1 protease (P5... -

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Basic information

Entry
Database: PDB / ID: 6ogt
TitleX-ray crystal structure of darunavir-resistant HIV-1 protease (P51) in complex with GRL-001
ComponentsProtease
KeywordsVIRAL PROTEIN/INHIBITOR / Inhibitor / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsBulut, H. / Hattori, S.I. / Aoki-Ogata, H. / Hayashi, H. / Aoki, M. / Ghosh, A.K. / Mitsuya, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Sci Rep / Year: 2020
Title: Single atom changes in newly synthesized HIV protease inhibitors reveal structural basis for extreme affinity, high genetic barrier, and adaptation to the HIV protease plasticity.
Authors: Bulut, H. / Hattori, S.I. / Aoki-Ogata, H. / Hayashi, H. / Das, D. / Aoki, M. / Davis, D.A. / Rao, K.V. / Nyalapatla, P.R. / Ghosh, A.K. / Mitsuya, H.
History
DepositionApr 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 28, 2021Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Oct 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: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7194
Polymers10,8761
Non-polymers8433
Water1,22568
1
A: Protease
hetero molecules

A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4378
Polymers21,7512
Non-polymers1,6866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area5090 Å2
ΔGint-21 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.071, 63.071, 82.196
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

21A-264-

HOH

31A-265-

HOH

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Components

#1: Protein Protease


Mass: 10875.717 Da / Num. of mol.: 1
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: O38893
#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-JDY / (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3-fluorophenyl)-3-hydroxybutan-2-yl]carbamate


Mass: 688.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H41FN4O7S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.15 M (NH4)2SO4, 0.1 M HEPES (pH 7.2), 20% (v/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.21→54.62 Å / Num. obs: 28980 / % possible obs: 96.3 % / Redundancy: 14.3 % / Net I/σ(I): 22.32
Reflection shellResolution: 1.21→1.25 Å / Num. unique obs: 28926

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TYR

5tyr


Resolution: 1.21→54.62 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.774 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.047 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1393 4.8 %RANDOM
Rwork0.192 ---
obs0.19265 27537 96.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.52 Å2
Refinement stepCycle: 1 / Resolution: 1.21→54.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms764 0 57 68 889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.014862
X-RAY DIFFRACTIONr_bond_other_d0.0090.018827
X-RAY DIFFRACTIONr_angle_refined_deg2.1241.7371177
X-RAY DIFFRACTIONr_angle_other_deg1.9951.6621923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8015102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.79522.63238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.80615138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.851155
X-RAY DIFFRACTIONr_chiral_restr0.1240.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02927
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02168
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5981.446405
X-RAY DIFFRACTIONr_mcbond_other1.5861.443404
X-RAY DIFFRACTIONr_mcangle_it2.462.175508
X-RAY DIFFRACTIONr_mcangle_other2.4622.176509
X-RAY DIFFRACTIONr_scbond_it2.6121.789451
X-RAY DIFFRACTIONr_scbond_other2.6121.79452
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0652.55662
X-RAY DIFFRACTIONr_long_range_B_refined5.33417.597856
X-RAY DIFFRACTIONr_long_range_B_other5.33717.621857
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.21→1.241 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 62 -
Rwork0.411 1417 -
obs--68.09 %

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