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- PDB-6o57: Crystal Structure of multi-drug resistant HIV-1 protease PR-S17 w... -

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Basic information

Entry
Database: PDB / ID: 6o57
TitleCrystal Structure of multi-drug resistant HIV-1 protease PR-S17 with a substrate analog p2-NC in P41
ComponentsHIV-1 protease
KeywordsHYDROLASE / Viral Protein / HIV PROTEASE
Function / homology
Function and homology information


aspartic-type endopeptidase activity / 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 / FORMIC ACID / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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)22,5387
Polymers21,5832
Non-polymers9555
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-23 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.881, 54.881, 82.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.87 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 29.5% PEG 4000, 0.2M ammonium acetate and 0.1M sodium acetate buffer at pH 4.6

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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: 1.71→50 Å / Num. obs: 26117 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.031 / Χ2: 1.007 / Net I/σ(I): 21.2
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2508 / CC1/2: 0.817 / Rpim(I) all: 0.28 / Χ2: 1.003 / % possible all: 95.2

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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: 1.71→27.46 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.711 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.108 / ESU R Free: 0.107
Details: initially refined by SHELX-2014 but moved to REFMAC during later cycles of refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1262 4.8 %RANDOM
Rwork0.1983 ---
obs0.19984 24824 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.735 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å2-0 Å2-0 Å2
2--0.71 Å20 Å2
3----1.41 Å2
Refinement stepCycle: 1 / Resolution: 1.71→27.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 66 78 1666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0141702
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171664
X-RAY DIFFRACTIONr_angle_refined_deg2.2061.6992327
X-RAY DIFFRACTIONr_angle_other_deg1.1711.683897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9245221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41822.77872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32615294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.791510
X-RAY DIFFRACTIONr_chiral_restr0.1410.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021922
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02300
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_it3.1243.318842
X-RAY DIFFRACTIONr_mcbond_other3.1223.317843
X-RAY DIFFRACTIONr_mcangle_it4.14.9511059
X-RAY DIFFRACTIONr_mcangle_other4.0984.951060
X-RAY DIFFRACTIONr_scbond_it3.9663.702860
X-RAY DIFFRACTIONr_scbond_other3.9783.71853
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.875.3831263
X-RAY DIFFRACTIONr_long_range_B_refined6.82237.8671664
X-RAY DIFFRACTIONr_long_range_B_other6.80537.7941656
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.709→1.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 79 -
Rwork0.286 1732 -
obs--93.3 %
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)
10.42550.0537-0.10060.1551-0.40821.0816-0.0501-0.1676-0.0110.0138-0.0501-0.0333-0.04470.11060.10030.01310.018-0.01750.0807-0.00680.064872.690612.159718.4754
20.14440.1063-0.37820.4284-0.20181.0125-0.05370.0106-0.0322-0.1738-0.0492-0.01710.1074-0.04540.10290.07910.0199-0.0070.0161-0.01860.06570.17169.676-3.3351
35.94494.09513.4125.58652.1331.97990.04730.0484-0.01-0.0278-0.0748-0.1020.02990.04580.02750.08170.0367-0.00810.08830.02070.117167.383613.98647.9264
40.70860.03810.52550.6748-0.00361.511-0.00240.02680.0492-0.0739-0.12120.0201-0.0966-0.03640.12360.036-0.0069-0.00180.0649-0.01420.124370.867313.06968.3152
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 99
2X-RAY DIFFRACTION2B1 - 99
3X-RAY DIFFRACTION3B201
4X-RAY DIFFRACTION4A101
5X-RAY DIFFRACTION4B202 - 204
6X-RAY DIFFRACTION4A201 - 239
7X-RAY DIFFRACTION4B301 - 339

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