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- PDB-6o5x: Crystal Structure of multi-drug resistant HIV-1 protease PR-S17 w... -

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Basic information

Entry
Database: PDB / ID: 6o5x
TitleCrystal Structure of multi-drug resistant HIV-1 protease PR-S17 with substrate analog CA-p2
ComponentsHIV-1 protease PR-S17
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-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl- L-alanyl-L-norleucinamide / Chem-0Q4 / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAgniswamy, J. / Wang, Y.-F. / 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 4, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 protease PR-S17
B: HIV-1 protease PR-S17
C: HIV-1 protease PR-S17
D: HIV-1 protease PR-S17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,28119
Polymers43,1664
Non-polymers2,11515
Water3,063170
1
A: HIV-1 protease PR-S17
B: HIV-1 protease PR-S17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,65210
Polymers21,5832
Non-polymers1,0698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-75 kcal/mol
Surface area9860 Å2
MethodPISA
2
C: HIV-1 protease PR-S17
D: HIV-1 protease PR-S17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6299
Polymers21,5832
Non-polymers1,0467
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-84 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.704, 60.358, 66.476
Angle α, β, γ (deg.)90.00, 90.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HIV-1 protease PR-S17


Mass: 10791.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: I7BFC3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-0Q4 / N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl-L-alanyl-L-norleucinamide / Inhibitor analogues of CA-p2


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 833.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H70N11O8
References: N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl- L-alanyl-L-norleucinamide
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 2.1M Sodium chloride, 0.1M HEPES pH 7.6

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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: MARMOSAIC 300 mm CCD / 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: 1.7→50 Å / Num. obs: 46434 / % possible obs: 99.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.045 / Net I/σ(I): 17.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 4633 / CC1/2: 0.886 / Rpim(I) all: 0.242 / Rsym value: 0.418 / Χ2: 1.004 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T2Z

5t2z


Resolution: 1.7→34.53 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21179 2291 4.9 %RANDOM
Rwork0.17581 ---
obs0.17766 44127 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.102 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å2-0.58 Å2
2---0.13 Å20 Å2
3---0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.7→34.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3044 0 131 170 3345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0193296
X-RAY DIFFRACTIONr_bond_other_d00.023408
X-RAY DIFFRACTIONr_angle_refined_deg2.2182.0214491
X-RAY DIFFRACTIONr_angle_other_deg3.59537818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0995409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.29924.53117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09115556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9471520
X-RAY DIFFRACTIONr_chiral_restr0.1410.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213685
X-RAY DIFFRACTIONr_gen_planes_other0.020.02717
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_it2.1331.7891630
X-RAY DIFFRACTIONr_mcbond_other2.1321.7891630
X-RAY DIFFRACTIONr_mcangle_it3.0182.6712038
X-RAY DIFFRACTIONr_mcangle_other3.0172.6712039
X-RAY DIFFRACTIONr_scbond_it3.6092.2391666
X-RAY DIFFRACTIONr_scbond_other3.6082.2391667
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4013.1852453
X-RAY DIFFRACTIONr_long_range_B_refined6.44714.9553276
X-RAY DIFFRACTIONr_long_range_B_other6.44914.8473235
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 149 -
Rwork0.186 3081 -
obs--94.94 %

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