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- PDB-6o5a: Crystal Structure of multi-drug resistant HIV-1 protease PR-S17 w... -

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Basic information

Entry
Database: PDB / ID: 6o5a
TitleCrystal Structure of multi-drug resistant HIV-1 protease PR-S17 with a substrate analog p2-NC in P61
ComponentsHIV-1 protease
KeywordsHYDROLASE / Viral Protein / HIV PROTEASE
Function / homology
Function and homology information


host multivesicular body / aspartic-type endopeptidase activity / virion membrane / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide / Chem-2NC / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsWang, Y.-F. / Agniswamy, J. / Weber, I.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM062920 United States
CitationJournal: Acs Omega / Year: 2019
Title: Highly Drug-Resistant HIV-1 Protease Mutant PRS17 Shows Enhanced Binding to Substrate Analogues.
Authors: Agniswamy, J. / Kneller, D.W. / Brothers, R. / Wang, Y.F. / Harrison, R.W. / Weber, I.T.
History
DepositionMar 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Structure summary / Category: pdbx_molecule_features
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)22,4464
Polymers21,5832
Non-polymers8632
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-25 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.833, 63.833, 83.039
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 HIV-1 protease


Mass: 10791.594 Da / Num. of mol.: 2 / Mutation: M46L, G48V, C67A, V77I, A82S, I93L, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7BFC3
#2: Chemical ChemComp-2NC / N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide / p2/NC


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 770.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68N11O8
References: N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 35% TacsimateTM, pH 7.0 (Hampton Research Corp., Aliso Viejo, CA). Tacsimate contains 1.83 M malonic acid, 0.25 M ammonium citrate tribasic, 0.12 M succinic acid, 0.3 M DL-malic acid, 0.4 M ...Details: 35% TacsimateTM, pH 7.0 (Hampton Research Corp., Aliso Viejo, CA). Tacsimate contains 1.83 M malonic acid, 0.25 M ammonium citrate tribasic, 0.12 M succinic acid, 0.3 M DL-malic acid, 0.4 M sodium acetate trihydrate, 0.5 M sodium formate, and 0.16 M ammonium tartrate dibasic.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 21945 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.029 / Χ2: 1 / Net I/σ(I): 16.9
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2 / Num. unique obs: 1989 / CC1/2: 0.641 / Rpim(I) all: 0.34 / Χ2: 1.004 / % possible all: 89.2

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0222refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SGU

1sgu


Resolution: 1.67→33.22 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.245 / SU ML: 0.078 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.109
Details: initially refined by SHELX-2014 but moved to REFMAC during later cycles of refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.21617 1076 4.9 %RANDOM
Rwork0.17554 ---
obs0.17753 20830 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.165 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.67→33.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 60 125 1707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0141722
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171706
X-RAY DIFFRACTIONr_angle_refined_deg2.2381.7032362
X-RAY DIFFRACTIONr_angle_other_deg1.1241.6923997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6385226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.622.60373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62215299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.971510
X-RAY DIFFRACTIONr_chiral_restr0.1250.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021920
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02306
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0992.334838
X-RAY DIFFRACTIONr_mcbond_other2.0992.335837
X-RAY DIFFRACTIONr_mcangle_it2.9013.491053
X-RAY DIFFRACTIONr_mcangle_other2.93.491054
X-RAY DIFFRACTIONr_scbond_it3.3142.805884
X-RAY DIFFRACTIONr_scbond_other3.3132.805884
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.24.0511299
X-RAY DIFFRACTIONr_long_range_B_refined6.08227.4511671
X-RAY DIFFRACTIONr_long_range_B_other6.06427.3081659
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.671→1.714 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 94 -
Rwork0.263 1349 -
obs--87.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.05410.14520.03320.8426-0.39540.6641-0.02920.02270.0183-0.09010.07890.02960.0712-0.0196-0.04970.0682-0.0124-0.00930.01490.01120.070323.98646.6067-5.7488
20.0844-0.1844-0.04150.9427-0.41920.6196-0.0344-0.0272-0.02590.08990.07880.0331-0.0656-0.013-0.04440.070.01170.01090.01380.00790.071324.0087-6.618711.7915
32.3847-0.3465-0.52251.51724.236511.9191-0.0890.00970.0039-0.04790.00270.0294-0.1512-0.02460.08630.0992-0.00390.00080.03640.02090.105519.17910.80133.1828
40.2624-0.10930.05471.1639-0.68740.5563-0.01460.0199-0.01440.00010.05890.0229-0.0007-0.061-0.04430.0457-0.00780.0040.0267-0.00690.03924.9655-0.02063.2909
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 99
2X-RAY DIFFRACTION2B1 - 99
3X-RAY DIFFRACTION3A201
4X-RAY DIFFRACTION4B101
5X-RAY DIFFRACTION4A301 - 364
6X-RAY DIFFRACTION4B201 - 261

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