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- PDB-4q5m: D30N tethered HIV-1 protease dimer/saquinavir complex -

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Basic information

Entry
Database: PDB / ID: 4q5m
TitleD30N tethered HIV-1 protease dimer/saquinavir complex
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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: 1.795 Å
AuthorsPrashar, V. / Bihani, S.C. / Ferrer, J.L. / Hosur, M.V.
CitationJournal: Chem.Biol.Drug Des. / Year: 2015
Title: Structural Basis of Why Nelfinavir-Resistant D30N Mutant of HIV-1 Protease Remains Susceptible to Saquinavir.
Authors: Prashar, V. / Bihani, S.C. / Ferrer, J.L. / Hosur, M.V.
History
DepositionApr 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / 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 / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name / _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
Revision 1.3Nov 8, 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: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5722
Polymers21,9011
Non-polymers6711
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.840, 62.840, 82.490
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


Mass: 21900.789 Da / Num. of mol.: 1 / Mutation: D30N, C95M, D1030N, C1095A
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.: 93 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHIMERA PROTEIN WITH LINKER GLY-GLY-SER-SER-GLY (NUMBERED A100 TO A104) THAT COVALENTLY LINK SUB- ...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.

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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: 2.15 Å3/Da / Density % sol: 42.71 %
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: ESRF / Beamline: BM30A / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.79→45.426 Å / Num. all: 17298 / Num. obs: 17150 / % possible obs: 99.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.6
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2740 / % possible all: 98.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1LV1

1lv1


Resolution: 1.795→45.4 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 858 5 %RANDOM
Rwork0.2061 ---
all0.2076 17297 --
obs0.2076 17148 99.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.795→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 49 93 1656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071665
X-RAY DIFFRACTIONf_angle_d1.0952267
X-RAY DIFFRACTIONf_dihedral_angle_d13.573635
X-RAY DIFFRACTIONf_chiral_restr0.069270
X-RAY DIFFRACTIONf_plane_restr0.005276
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.795-1.90740.33741410.2676267898
1.9074-2.05470.29071420.2318270599
2.0547-2.26150.2781430.2236270999
2.2615-2.58870.24441430.2191272799
2.5887-3.26130.2241440.21622735100
3.2613-45.44050.19981450.1777273699

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