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- PDB-6ixd: X-ray crystal structure of bPI-11 hiv-1 protease complex -

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Basic information

Entry
Database: PDB / ID: 6ixd
TitleX-ray crystal structure of bPI-11 hiv-1 protease complex
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV-1 protease / 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
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1 Å
AuthorsAdachi, M. / Hidaka, K.
CitationJournal: Bioconjug.Chem. / Year: 2019
Title: Acquired Removability of Aspartic Protease Inhibitors by Direct Biotinylation.
Authors: Hidaka, K. / Adachi, M. / Tsuda, Y.
History
DepositionDec 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8589
Polymers21,4812
Non-polymers1,3777
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-44 kcal/mol
Surface area9800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.302, 86.010, 46.549
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5RZ08, HIV-1 retropepsin

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Non-polymers , 5 types, 361 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-B0F / (4R)-3-[(2S,3S)-3-[2-[4-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]-2,6-dimethyl-phenoxy]ethanoylamino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-N-[(1S,2R)-2-oxidanyl-2,3-dihydro-1H-inden-1-yl]-1,3-thiazolidine-4-carboxamide


Type: peptide-like / Mass: 873.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H56N6O8S2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50mM sodium acetate buffer (pH 5.0), 20% saturated ammonium sulfate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→46.6 Å / Num. obs: 126583 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 29.3
Reflection shellResolution: 1→1.04 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 12353 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3FX5

3fx5


Resolution: 1→43.005 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 10.55
RfactorNum. reflection% reflectionSelection details
Rfree0.1501 6326 5 %Random selection
Rwork0.1316 ---
obs0.1325 126508 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1→43.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 90 354 1956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072200
X-RAY DIFFRACTIONf_angle_d1.3373011
X-RAY DIFFRACTIONf_dihedral_angle_d12.146844
X-RAY DIFFRACTIONf_chiral_restr0.075346
X-RAY DIFFRACTIONf_plane_restr0.008370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.01130.2112020.2053839X-RAY DIFFRACTION96
1.0113-1.02320.18132050.17973895X-RAY DIFFRACTION99
1.0232-1.03570.17322100.15513989X-RAY DIFFRACTION99
1.0357-1.04880.16052090.13683957X-RAY DIFFRACTION100
1.0488-1.06260.14362070.12463955X-RAY DIFFRACTION100
1.0626-1.07720.11622080.11623953X-RAY DIFFRACTION100
1.0772-1.09260.12252090.10493967X-RAY DIFFRACTION100
1.0926-1.10890.10632100.10283989X-RAY DIFFRACTION100
1.1089-1.12620.10972080.10213941X-RAY DIFFRACTION100
1.1262-1.14470.1072110.09854001X-RAY DIFFRACTION100
1.1447-1.16440.1052110.09564030X-RAY DIFFRACTION100
1.1644-1.18560.11422080.09333936X-RAY DIFFRACTION100
1.1856-1.20840.1052100.0963995X-RAY DIFFRACTION100
1.2084-1.23310.11562080.09893970X-RAY DIFFRACTION100
1.2331-1.25990.12092110.0993993X-RAY DIFFRACTION100
1.2599-1.28920.10572100.10173994X-RAY DIFFRACTION100
1.2892-1.32140.11612100.10343991X-RAY DIFFRACTION100
1.3214-1.35720.11632110.10434014X-RAY DIFFRACTION100
1.3572-1.39710.12932090.10963975X-RAY DIFFRACTION100
1.3971-1.44220.11712120.10854017X-RAY DIFFRACTION100
1.4422-1.49370.12292120.11544015X-RAY DIFFRACTION100
1.4937-1.55350.15222110.1144030X-RAY DIFFRACTION100
1.5535-1.62430.13362130.12144033X-RAY DIFFRACTION100
1.6243-1.70990.14542100.12544004X-RAY DIFFRACTION100
1.7099-1.8170.16812130.1364046X-RAY DIFFRACTION100
1.817-1.95730.14392150.13374069X-RAY DIFFRACTION100
1.9573-2.15430.13242120.13164055X-RAY DIFFRACTION100
2.1543-2.4660.17392160.15244082X-RAY DIFFRACTION100
2.466-3.10680.18232180.16134143X-RAY DIFFRACTION100
3.1068-43.04480.18162270.14874304X-RAY DIFFRACTION100

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