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- PDB-2fle: Structural analysis of asymmetric inhibitor bound to the HIV-1 Pr... -

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Basic information

Entry
Database: PDB / ID: 2fle
TitleStructural analysis of asymmetric inhibitor bound to the HIV-1 Protease V82A mutant
Componentspol protein
Keywordshydrolase/hydrolase inhibitor / HIV-1 protease / inhibitor / resistance / induced fit / hydrolase-hydrolase inhibitor COMPLEX
Function / homology
Function and homology information


aspartic-type endopeptidase activity
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-AI / : / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsClemente, J.C. / Robbins, A. / Dunn, B.M. / Sussman, F.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Design, synthesis, evaluation, and crystallographic-based structural studies of HIV-1 protease inhibitors with reduced response to the V82A mutation.
Authors: Clemente, J.C. / Robbins, A. / Grana, P. / Paleo, M.R. / Correa, J.F. / Villaverde, M.C. / Sardina, F.J. / Govindasamy, L. / Agbandje-McKenna, M. / McKenna, R. / Dunn, B.M. / Sussman, F.
History
DepositionJan 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pol protein
B: pol protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3884
Polymers21,4952
Non-polymers8932
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-28 kcal/mol
Surface area9060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.195, 62.195, 82.752
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsThe asymetric unit consist of the HIV protease homodimer

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Components

#1: Protein pol protein


Mass: 10747.688 Da / Num. of mol.: 2 / Fragment: HIV-1 protease / Mutation: V82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star DE3 pLysS / References: GenBank: 33304696, UniProt: Q9J2R0*PLUS
#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-AI / (2S,2'S)-N,N'-[(2S,3S,4S,5S)-1-CYCLOHEXYL-3,4-DIHYDROXY-6-PHENYLHEXANE-2,5-DIYL]BIS[3-METHYL-2-({[METHYL(PYRIDIN-2-YLMETHYL)AMINO]CARBONYL}AMINO)BUTANAMIDE]


Mass: 801.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H64N8O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M Sodium Cacodylate pH 6.5, 0.2 M Magnesium Acetate tetrahydrate, 20% Polyethylene Glycol 8000. (Hampton Research Crystal Screen Solution #18), VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 14460 / Num. obs: 14371 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.24 / Net I/σ(I): 22.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1424 / Χ2: 0.993 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1hxw

1hxw


Resolution: 1.9→19.77 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 481957.719 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 652 5 %RANDOM
Rwork0.199 ---
obs0.207 12939 90 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.034 Å2 / ksol: 0.409 e/Å3
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.61 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 64 77 1649
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it2.782
X-RAY DIFFRACTIONc_scbond_it3.182
X-RAY DIFFRACTIONc_scangle_it4.622.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 88 4.9 %
Rwork0.225 1724 -
obs-1812 75.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2water.topwater_rep.param
X-RAY DIFFRACTION3INH1_sync2.topINH1_sync2.param
X-RAY DIFFRACTION4GOL.topGOL.param

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