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- PDB-6u7p: HIV-1 wild type protease with GRL-03119A, with phenyl-boronic-aci... -

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Basic information

Entry
Database: PDB / ID: 6u7p
TitleHIV-1 wild type protease with GRL-03119A, with phenyl-boronic-acid as P2'-ligand and with a hexahydro-4H-furo-pyran as the P2-ligand
ComponentsProtease
KeywordsVIRAL PROTEIN / ASPARTIC ACID PROTEASE / HIV-1 PROTEASE INHIBITOR OF GRL-03119A / BORONIC ACID
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
Chem-B4R / FORMIC ACID / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.13 Å
AuthorsWang, Y.-F. / Kneller, D.W. / Weber, I.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI150466 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)AI150461 United States
CitationJournal: Chemmedchem / Year: 2019
Title: Potent HIV-1 Protease Inhibitors Containing Carboxylic and Boronic Acids: Effect on Enzyme Inhibition and Antiviral Activity and Protein-Ligand X-ray Structural Studies.
Authors: Ghosh, A.K. / Xia, Z. / Kovela, S. / Robinson, W.L. / Johnson, M.E. / Kneller, D.W. / Wang, Y.F. / Aoki, M. / Takamatsu, Y. / Weber, I.T. / Mitsuya, H.
History
DepositionSep 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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)22,41011
Polymers21,4812
Non-polymers9299
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-80 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.491, 86.097, 46.086
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protease


Mass: 10740.677 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, 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: Q5RZ08

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Non-polymers , 6 types, 231 molecules

#2: Chemical ChemComp-B4R / {4-[{(2R,3S)-3-[({[(3aS,4S,7aR)-hexahydro-4H-furo[2,3-b]pyran-4-yl]oxy}carbonyl)amino]-2-hydroxy-4-phenylbutyl}(2-methylpropyl)sulfamoyl]phenyl}boronic acid


Mass: 590.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H39BN2O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 1.3 M sodium chloride, 0.1 M sodium acetate pH 6.2

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→50 Å / Num. obs: 79649 / % possible obs: 90.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.026 / Rrim(I) all: 0.066 / Χ2: 0.995 / Net I/σ(I): 14.8 / Num. measured all: 456362
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.13-1.1720.44543840.7350.3410.5641.00150.7
1.17-1.223.20.38362680.8360.2380.4550.99272.4
1.22-1.275.40.31580840.9440.1410.3460.9993.2
1.27-1.346.40.2584820.9750.1040.2720.99297.9
1.34-1.426.20.17885640.9840.0760.1950.99198.4
1.42-1.5360.12286210.9890.0530.1330.99898.6
1.53-1.696.60.08586660.9950.0350.0921.00599.3
1.69-1.936.20.06587450.9960.0280.0710.99999.5
1.93-2.436.40.05587540.9960.0230.060.99198.7
2.43-506.30.05390810.9960.0230.0580.99598.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.31 Å34.67 Å
Translation5.31 Å34.67 Å

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Processing

Software
NameVersionClassification
HKL-20000.716.1data scaling
PHASER4.064 Datablock id: mmcif_pdbx.dicphasing
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-20000.716.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NU3

3nu3


Resolution: 1.13→34.69 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.752 / SU ML: 0.016 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.027 / Details: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1405 3888 4.9 %RANDOM
Rwork0.125 ---
obs0.1258 75718 90.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 157.07 Å2 / Biso mean: 16.059 Å2 / Biso min: 6.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0 Å2
2--0.39 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 1.13→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 97 222 1831
Biso mean--13.81 25.26 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0131819
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171859
X-RAY DIFFRACTIONr_angle_refined_deg2.5171.7092511
X-RAY DIFFRACTIONr_angle_other_deg1.4781.6324357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9935250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.35622.94168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.98415341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.602159
X-RAY DIFFRACTIONr_chiral_restr0.550.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021994
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02339
X-RAY DIFFRACTIONr_rigid_bond_restr6.27433678
LS refinement shellResolution: 1.131→1.16 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 164 -
Rwork0.366 2869 -
all-3033 -
obs--47.44 %

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