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- PDB-3n3i: Crystal Structure of G48V/C95F tethered HIV-1 Protease/Saquinavir... -

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Basic information

Entry
Database: PDB / ID: 3n3i
TitleCrystal Structure of G48V/C95F tethered HIV-1 Protease/Saquinavir complex
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV-1 protease / Saquinavir / Drug Resistance / tethered-dimer / fusion protein / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase activity / 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 / DNA binding / zinc ion binding / identical protein 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
Saquinavir / Chem-ROC / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.501 Å
AuthorsPrashar, V. / Bihani, S.C. / Das, A. / Rao, D.R. / Hosur, M.V.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Insights into the mechanism of drug resistance: X-ray structure analysis of G48V/C95F tethered HIV-1 protease dimer/saquinavir complex
Authors: Prashar, V. / Bihani, S.C. / Das, A. / Rao, D.R. / Hosur, M.V.
History
DepositionMay 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Aug 9, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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

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Assembly

Deposited unit
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7502
Polymers22,0791
Non-polymers6711
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.410, 62.410, 83.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protease / Retropepsin / PR


Mass: 22078.994 Da / Num. of mol.: 1 / Fragment: UNP residues 489-587 / Mutation: G48V, G1048V, C95F, C1095F
Source method: isolated from a genetically manipulated source
Details: Chimera protein with LINKER Gly-Gly-Ser-Ser-Gly (numbered A100 to A104) that covalently link sub-unit A with sub-unit B in the tethered dimer.
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: group M subtype B (isolate HXB2) / Gene: gag-pol / Plasmid: pET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04585, HIV-1 retropepsin
#2: Chemical ChemComp-ROC / (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide / Fortovase / SAQUINAVIR / RO 31-8959


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 670.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H50N6O5 / References: Saquinavir / Comment: medication, antiretroviral*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR SAQUINAVIR (ROC) IS A HYDROXYETHYLAMINE CONTAINING TRANSITION STATE MIMETIC. IT IS ...THE INHIBITOR SAQUINAVIR (ROC) IS A HYDROXYETHYLAMINE CONTAINING TRANSITION STATE MIMETIC. IT IS REFERRED AS SQV IN THE ARTICLE.
Sequence detailsTHE LINKER IS DISORDERED. SO THERE ARE NO COORDINATES FOR THE LINKER GGSSG.

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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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1-5% saturated Ammonium Sulfate, 200/100mM Phosphate/Citrate Buffer, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→32.981 Å / Num. all: 6307 / Num. obs: 6307 / % possible obs: 98.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 39.32 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 6 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 3.9 / Num. unique all: 900 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6_289)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.501→32.981 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 2.05 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 288 4.57 %RANDOM
Rwork0.216 ---
obs0.2177 6304 98.61 %-
all-6307 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.89 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 101.15 Å2 / Biso mean: 42.094 Å2 / Biso min: 14.94 Å2
Baniso -1Baniso -2Baniso -3
1-2.7529 Å2-0 Å2-0 Å2
2--2.7529 Å2-0 Å2
3----5.5058 Å2
Refinement stepCycle: LAST / Resolution: 2.501→32.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1529 0 49 60 1638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071611
X-RAY DIFFRACTIONf_angle_d1.12189
X-RAY DIFFRACTIONf_dihedral_angle_d16.909606
X-RAY DIFFRACTIONf_chiral_restr0.066262
X-RAY DIFFRACTIONf_plane_restr0.005270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5007-3.15020.34771440.25462974X-RAY DIFFRACTION98
3.1502-32.98380.21911440.19833042X-RAY DIFFRACTION99

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