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- PDB-3th9: Crystal Structure of HIV-1 Protease Mutant Q7K V32I L63I with a c... -

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Basic information

Entry
Database: PDB / ID: 3th9
TitleCrystal Structure of HIV-1 Protease Mutant Q7K V32I L63I with a cyclic sulfonamide inhibitor
ComponentsGag-Pol polyprotein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / enzyme inhibition / aspartic protease / HIV/AIDS / conformational change / Amprenavir / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA 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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / 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-9Y9 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 lw12.3 isolate
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsOrth, P.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Design, Synthesis, and X-ray Crystallographic Analysis of a Novel Class of HIV-1 Protease Inhibitors.
Authors: Ganguly, A.K. / Alluri, S.S. / Caroccia, D. / Biswas, D. / Wang, C.H. / Kang, E. / Zhang, Y. / McPhail, A.T. / Carroll, S.S. / Burlein, C. / Munshi, V. / Orth, P. / Strickland, C.
History
DepositionAug 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,5954
Polymers21,6102
Non-polymers9852
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-22 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.680, 85.890, 46.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Gag-Pol polyprotein / Protease


Mass: 10804.808 Da / Num. of mol.: 2 / Fragment: HIV protease / Mutation: Q7K V32I L63I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 lw12.3 isolate
Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P0C6F2, HIV-1 retropepsin
#2: Chemical ChemComp-9Y9 / tert-butyl {(2S,3R)-4-[(4S)-7-fluoro-4-methyl-1,1-dioxido-4,5-dihydro-1,2-benzothiazepin-2(3H)-yl]-3-hydroxy-1-phenylbutan-2-yl}carbamate


Mass: 492.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H33FN2O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1 M sodium acetate buffer, 0.4M NaCl, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2011
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.34→85.89 Å / Num. obs: 51837 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.34→1.41 Å / % possible all: 96

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
SCALAdata scaling
AMoREphasing
BUSTER2.9.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→48.45 Å / Cor.coef. Fo:Fc: 0.9539 / Cor.coef. Fo:Fc free: 0.9571 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1904 1082 2.09 %RANDOM
Rwork0.181 ---
all0.1812 53126 --
obs0.1812 51798 97.2 %-
Displacement parametersBiso max: 73.92 Å2 / Biso mean: 18.6099 Å2 / Biso min: 7.52 Å2
Baniso -1Baniso -2Baniso -3
1--5.6623 Å20 Å20 Å2
2--2.6895 Å20 Å2
3---2.9728 Å2
Refine analyzeLuzzati coordinate error obs: 0.149 Å
Refinement stepCycle: LAST / Resolution: 1.34→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 0 68 238 1807
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d535SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes223HARMONIC5
X-RAY DIFFRACTIONt_it1606HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion227SEMIHARMONIC5
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_contact1994SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1606HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2189HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion4.12
X-RAY DIFFRACTIONt_other_torsion13.27
LS refinement shellResolution: 1.34→1.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2388 77 2.09 %
Rwork0.2138 3613 -
all0.2143 3690 -
obs--97.2 %

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