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- PDB-2a4f: Synthesis and Activity of N-Axyl Azacyclic Urea HIV-1 Protease In... -

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Basic information

Entry
Database: PDB / ID: 2a4f
TitleSynthesis and Activity of N-Axyl Azacyclic Urea HIV-1 Protease Inhibitors with High Potency Against Multiple Drug Resistant Viral Strains.
ComponentsPol polyprotein
KeywordsHYDROLASE / HIV protease / aza-cyclic urea
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-AAU / V-1 protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsZhao, C. / Sham, H. / Sun, M. / Lin, S. / Stoll, V. / Stewart, K.D. / Mo, H. / Vasavanonda, S. / Saldivar, A. / McDonald, E.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2005
Title: Synthesis and activity of N-acyl azacyclic urea HIV-1 protease inhibitors with high potency against multiple drug resistant viral strains
Authors: Zhao, C. / Sham, H.L. / Sun, M. / Stoll, V.S. / Stewart, K.D. / Lin, S. / Mo, H. / Vasavanonda, S. / Saldivar, A. / Park, C. / McDonald, E.J. / Marsh, K.C. / Klein, L.L. / Kempf, D.J. / Norbeck, D.W.
History
DepositionJun 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pol polyprotein
B: Pol polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2493
Polymers21,6082
Non-polymers6421
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-31 kcal/mol
Surface area9450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.008, 85.742, 46.646
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 Pol polyprotein


Mass: 10803.756 Da / Num. of mol.: 2 / Fragment: HIV protease
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Q2G8, HIV-1 retropepsin
#2: Chemical ChemComp-AAU / (5R,6R)-5-BENZYL-6-HYDROXY-2,4-BIS(4-HYDROXY-3-METHOXYBENZYL)-1-[3-(4-HYDROXYPHENYL)PROPANOYL]-1,2,4-TRIAZEPAN-3-ONE


Mass: 641.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H39N3O8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: acetate buffer, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 24163 / Num. obs: 18310 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 10.8 Å2
Reflection shellResolution: 1.9→2.02 Å / % possible all: 95.1

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Processing

Software
NameVersionClassification
CNX2000refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→42.87 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 578535.39 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: waters picked at level greater than 2.0
RfactorNum. reflection% reflectionSelection details
Rfree0.336 1269 6.9 %RANDOM
Rwork0.298 ---
obs-18310 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.104671 e/Å3
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.62 Å20 Å20 Å2
2---2.15 Å20 Å2
3----0.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.9→42.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 47 84 1645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 179 6 %
Rwork0.307 2780 -
obs--95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramlig.top
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4lig.par

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