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- PDB-6b3f: Crystal Structure of HIV Protease complexed with N-(3-fluoro-2-(2... -

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Basic information

Entry
Database: PDB / ID: 6b3f
TitleCrystal Structure of HIV Protease complexed with N-(3-fluoro-2-(2-((2S,5S)-5-methyl-1-(phenylsulfonyl)piperazin-2-yl)ethyl)phenyl)-3,3-bis(4-fluorophenyl)propanamide
ComponentsHIV-1 Protease
KeywordsVIRAL PROTEIN/INHIBITOR / HIV / protease / VIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-CKV / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.46 Å
AuthorsSu, H.P.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Design and Synthesis of Piperazine Sulfonamide Cores Leading to Highly Potent HIV-1 Protease Inhibitors.
Authors: Bungard, C.J. / Williams, P.D. / Schulz, J. / Wiscount, C.M. / Holloway, M.K. / Loughran, H.M. / Manikowski, J.J. / Su, H.P. / Bennett, D.J. / Chang, L. / Chu, X.J. / Crespo, A. / Dwyer, M.P. ...Authors: Bungard, C.J. / Williams, P.D. / Schulz, J. / Wiscount, C.M. / Holloway, M.K. / Loughran, H.M. / Manikowski, J.J. / Su, H.P. / Bennett, D.J. / Chang, L. / Chu, X.J. / Crespo, A. / Dwyer, M.P. / Keertikar, K. / Morriello, G.J. / Stamford, A.W. / Waddell, S.T. / Zhong, B. / Hu, B. / Ji, T. / Diamond, T.L. / Bahnck-Teets, C. / Carroll, S.S. / Fay, J.F. / Min, X. / Morris, W. / Ballard, J.E. / Miller, M.D. / McCauley, J.A.
History
DepositionSep 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: HIV-1 Protease
B: HIV-1 Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3386
Polymers21,6102
Non-polymers7284
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-50 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.550, 85.940, 46.490
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 HIV-1 Protease /


Mass: 10804.808 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Production host: Human immunodeficiency virus 1 / References: UniProt: P04587, HIV-1 retropepsin
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CKV / N-(3-fluoro-2-{2-[(2S,5S)-5-methyl-1-(phenylsulfonyl)piperazin-2-yl]ethyl}phenyl)-3,3-bis(4-fluorophenyl)propanamide


Mass: 621.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34F3N3O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium acetate pH 5.0-5.5 300-500 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.463→21.38 Å / Num. obs: 263350 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 18.34 Å2 / Net I/σ(I): 18.9

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.46→21.38 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.062 / SU Rfree Blow DPI: 0.06 / SU Rfree Cruickshank DPI: 0.059
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2069 5.03 %RANDOM
Rwork0.183 ---
obs0.183 41153 99.2 %-
Displacement parametersBiso mean: 20.96 Å2
Baniso -1Baniso -2Baniso -3
1--3.5796 Å20 Å20 Å2
2--2.2372 Å20 Å2
3---1.3425 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: 1 / Resolution: 1.46→21.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 47 158 1721
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011597HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.212167HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d560SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC8
X-RAY DIFFRACTIONt_gen_planes235HARMONIC8
X-RAY DIFFRACTIONt_it1597HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion14.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion222SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1881SEMIHARMONIC4
LS refinement shellResolution: 1.46→1.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2172 138 5.06 %
Rwork0.2284 2591 -
all0.2279 2729 -
obs--90.19 %

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