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- PDB-4qgi: X-ray crystal structure of HIV-1 protease variant G48T/L89M in co... -

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Basic information

Entry
Database: PDB / ID: 4qgi
TitleX-ray crystal structure of HIV-1 protease variant G48T/L89M in complex with Saquinavir
ComponentsProtease
Keywordshydrolase/hydrolase inhibitor / Saquinavir / HIV Protease / 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 / 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 / host cell plasma membrane / virion membrane / structural molecule activity / 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
Saquinavir / Chem-ROC / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 lw12.3 isolate
MethodX-RAY DIFFRACTION / Resolution: 1.896 Å
AuthorsMahon, B.P. / McKenna, R. / Goldfarb, N.
CitationJournal: Biochemistry / Year: 2015
Title: Defective Hydrophobic Sliding Mechanism and Active Site Expansion in HIV-1 Protease Drug Resistant Variant Gly48Thr/Leu89Met: Mechanisms for the Loss of Saquinavir Binding Potency.
Authors: Goldfarb, N.E. / Ohanessian, M. / Biswas, S. / McGee, T.D. / Mahon, B.P. / Ostrov, D.A. / Garcia, J. / Tang, Y. / McKenna, R. / Roitberg, A. / Dunn, B.M.
History
DepositionMay 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 24, 2018Group: Refinement description / Category: refine / Item: _refine.pdbx_method_to_determine_struct
Revision 1.5Feb 28, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4954
Polymers21,7322
Non-polymers7632
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-27 kcal/mol
Surface area9530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.952, 67.168, 93.503
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segidB0

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Components

#1: Protein Protease / / Gag-Pol polyprotein / PR Retropepsin


Mass: 10865.847 Da / Num. of mol.: 2 / Fragment: HIV-1 Protease Chain A, unp residues 489-587 / Mutation: G48T, L89M
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) / Strain (production host): Bl21 Star DE3 PlysS / References: UniProt: P0C6F2, 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 / Saquinavir


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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Sodium citrate, 20% 2-propanol, 20% PEG 4000 , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5148 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationMonochromator: Varimax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5148 Å / Relative weight: 1
ReflectionResolution: 1.9→28.28 Å / Num. all: 15146 / Num. obs: 14599 / % possible obs: 96.5 % / Observed criterion σ(F): 24.6 / Observed criterion σ(I): 244.6 / Biso Wilson estimate: 19.99 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.9-1.97194.8
1.97-2.05198.6
2.05-2.14197.7
2.14-2.25197.6
2.25-2.39197.9
2.39-2.58197.1
2.58-2.84197.1
2.84-3.25196.8
3.25-4.09195.7
4.09-50191.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
CrystalCleardata collection
SHELXSphasing
RefinementResolution: 1.896→28.272 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 725 4.97 %Random
Rwork0.1871 ---
obs0.1901 14599 96.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.75 Å2 / Biso mean: 19.9396 Å2 / Biso min: 5.52 Å2
Refinement stepCycle: LAST / Resolution: 1.896→28.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 55 167 1744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081645
X-RAY DIFFRACTIONf_angle_d1.1592162
X-RAY DIFFRACTIONf_chiral_restr0.048256
X-RAY DIFFRACTIONf_plane_restr0.005274
X-RAY DIFFRACTIONf_dihedral_angle_d14.127608
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A888X-RAY DIFFRACTION6.317TORSIONAL
12B888X-RAY DIFFRACTION6.317TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8955-2.04180.32351410.22022707284896
2.0418-2.24720.27971450.20552759290498
2.2472-2.57220.27791440.20552769291398
2.5722-3.240.28711460.19422801294797
3.24-28.27530.18441490.16262838298794
Refinement TLS params.Method: refined / Origin x: 13.4726 Å / Origin y: -2.9731 Å / Origin z: -9.6509 Å
111213212223313233
T0.0709 Å2-0.0042 Å2-0.0047 Å2-0.0694 Å20.004 Å2--0.0747 Å2
L0.0779 °20.0421 °2-0.0117 °2-0.0557 °20.0509 °2--0.1069 °2
S-0.0053 Å °-0.0105 Å °0.0068 Å °0.0023 Å °-0.0175 Å °-0.0173 Å °0.0397 Å °-0.0041 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 99
2X-RAY DIFFRACTION1allB1 - 99
3X-RAY DIFFRACTION1allA1 - 101
4X-RAY DIFFRACTION1allA - B1 - 190
5X-RAY DIFFRACTION1allA102 - 1816

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