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- PDB-6mkl: X-ray crystal structure of darunavir-resistant-P51 HIV-1 protease... -

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Basic information

Entry
Database: PDB / ID: 6mkl
TitleX-ray crystal structure of darunavir-resistant-P51 HIV-1 protease in complex with GRL-142
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease-inhibitor complex / darunavir-resistance / P51 / GRL-142 / non-peptidic / HYDROLASE / HYDROLASE-HYDROLASE 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
Chem-7OA / Protease / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYedidi, R.S. / Hayashi, H. / Das, D. / Mitsuya, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Citation
Journal: To Be Published
Title: Structure-function analysis of darunavir-resistant-P51 HIV-1 protease in complex with GRL-142.
Authors: Yedidi, R.S. / Hayashi, H. / Das, D. / Mitsuya, H.
#1: Journal: J. Virol. / Year: 2010
Title: In vitro selection of highly darunavir-resistant and replication-competent HIV-1 variants by using a mixture of clinical HIV-1 isolates resistant to multiple conventional protease inhibitors.
Authors: Koh, Y. / Amano, M. / Towata, T. / Danish, M. / Leshchenko-Yashchuk, S. / Das, D. / Nakayama, M. / Tojo, Y. / Ghosh, A.K. / Mitsuya, H.
History
DepositionSep 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 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
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4583
Polymers21,7512
Non-polymers7071
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-24 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.284, 63.284, 82.072
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protease /


Mass: 10875.717 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: O38893, UniProt: A0A4P8EW36*PLUS
#2: Chemical ChemComp-7OA / (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-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]carbamate


Mass: 706.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40F2N4O7S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.15 M Ammonium sulfate 0.1 M HEPES (pH 6.8) 15% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 40129 / % possible obs: 98.3 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.28
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2843 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HLA

4hla


Resolution: 1.7→32.848 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 17.79
RfactorNum. reflection% reflection
Rfree0.1883 2005 5.02 %
Rwork0.1675 --
obs0.1686 39949 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→32.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 48 197 1773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091666
X-RAY DIFFRACTIONf_angle_d1.2882278
X-RAY DIFFRACTIONf_dihedral_angle_d16.813604
X-RAY DIFFRACTIONf_chiral_restr0.054262
X-RAY DIFFRACTIONf_plane_restr0.007278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.74260.21451470.19272704X-RAY DIFFRACTION98
1.7426-1.78970.17531350.17872669X-RAY DIFFRACTION98
1.7897-1.84230.20291500.1762664X-RAY DIFFRACTION98
1.8423-1.90180.20141140.17792750X-RAY DIFFRACTION98
1.9018-1.96980.18321550.16842725X-RAY DIFFRACTION99
1.9698-2.04860.19551490.16842674X-RAY DIFFRACTION99
2.0486-2.14180.17551320.17372685X-RAY DIFFRACTION98
2.1418-2.25470.19121280.16422758X-RAY DIFFRACTION99
2.2547-2.3960.19711560.17762700X-RAY DIFFRACTION99
2.396-2.58090.19241460.17952742X-RAY DIFFRACTION99
2.5809-2.84050.19371410.17872721X-RAY DIFFRACTION100
2.8405-3.25120.15221470.16612691X-RAY DIFFRACTION99
3.2512-4.09490.18671490.14842747X-RAY DIFFRACTION100
4.0949-32.85450.20121560.1592714X-RAY DIFFRACTION99

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