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- PDB-3em6: Crystal structure of I50L/A71V mutant of hiv-1 protease in comple... -

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Basic information

Entry
Database: PDB / ID: 3em6
TitleCrystal structure of I50L/A71V mutant of hiv-1 protease in complex with inhibitor darunavir
ComponentsProtease
KeywordsHYDROLASE / protease inhibitor / hyper susceptibility / drug resistance / hiv / darunavir / AIDS / Protease
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 / structural molecule activity / host cell plasma membrane / virion membrane / 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
Chem-017 / ACETATE ION / PHOSPHATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsRoyer, C.J. / King, N.M. / Prabu-Jeyabalan, M. / Ng, C. / Nalivaika, E.A. / Schiffer, C.A.
CitationJournal: To be Published
Title: Kinetic and structural studies on atazanavir specific I50L drug-resistant HIV-1 protease mutant.
Authors: Prabu-Jeyabalan, M. / Ng, C. / King, N.M. / Bandaranayake, R. / Nalivaika, E.A. / Schiffer, C.A.
History
DepositionSep 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,85911
Polymers21,6602
Non-polymers1,2009
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-59 kcal/mol
Surface area9110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.140, 57.891, 61.364
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protease / / Retropepsin / PR


Mass: 10829.816 Da / Num. of mol.: 2 / Fragment: UNP residues 491-589 / Mutation: Q7K, I50L, A71V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: HXB2 / Gene: gag-pol, HIV-1 subtype B / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: P03369, HIV-1 retropepsin
#2: Chemical ChemComp-017 / (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE / Darunavir / TMC114 / UIC-94017 / Darunavir


Mass: 547.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H37N3O7S / Details: Darunavir / Comment: medication, antiretroviral*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 28, 2004 / Details: Yale Mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 10762 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.092 / Χ2: 1.052 / Net I/σ(I): 11.443
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.180.46110271.127195.6
2.18-2.260.40310561.194196.8
2.26-2.370.34210461.146196.9
2.37-2.490.29110681.131197.1
2.49-2.650.22310661.136196.7
2.65-2.850.17510761.168197.2
2.85-3.140.11710681.057197.2
3.14-3.590.06810990.997197.4
3.59-4.520.04211140.827197.6
4.52-500.03611420.78194

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3.006data extraction
AMoREphasing
RefinementStarting model: 1F7A

1f7a


Resolution: 2.1→42.26 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.468 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.276 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 507 4.7 %RANDOM
Rwork0.186 ---
obs0.188 10740 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 48.64 Å2 / Biso mean: 6.32 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 75 108 1641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0221590
X-RAY DIFFRACTIONr_bond_other_d0.0010.021519
X-RAY DIFFRACTIONr_angle_refined_deg1.1512.0282179
X-RAY DIFFRACTIONr_angle_other_deg0.82533516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3155202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.1452552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45615241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.465157
X-RAY DIFFRACTIONr_chiral_restr0.0670.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021737
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02287
X-RAY DIFFRACTIONr_nbd_refined0.1780.2244
X-RAY DIFFRACTIONr_nbd_other0.1820.21526
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2715
X-RAY DIFFRACTIONr_nbtor_other0.0820.2952
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.213
X-RAY DIFFRACTIONr_mcbond_it0.4391.51286
X-RAY DIFFRACTIONr_mcbond_other0.0621.5418
X-RAY DIFFRACTIONr_mcangle_it0.48521616
X-RAY DIFFRACTIONr_scbond_it0.7223655
X-RAY DIFFRACTIONr_scangle_it1.0564.5563
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 31 -
Rwork0.234 721 -
all-752 -
obs--95.8 %
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)
11.58111.2221.6833.09340.16983.5737-0.05940.25240.1524-0.11220.02050.0417-0.1162-0.03520.0389-0.0261-0.0147-0.0226-0.01660.03-0.069820.36528.64932.362
217.4901-2.15273.1984.70470.2989.39340.19620.2455-0.9111-0.30820.14650.33660.76180.0199-0.34270.0431-0.0219-0.0138-0.0312-0.0487-0.036820.7545-4.77852.524
311.14681.70594.48155.73963.28443.03430.3319-0.4040.22410.225-0.18490.52320.01610.1627-0.147-0.04880.01780.0234-0.0807-0.0142-0.077719.460412.230514.9645
416.6113-4.57533.44946.38651.50335.41570.08450.2532-0.0167-0.1250.0966-0.7027-0.09030.4293-0.1811-0.0235-0.00360.047-0.05730.0134-0.049738.6161-2.11796.991
53.475-1.2721-0.44031.1304-0.10480.16220.02980.0157-0.0304-0.0409-0.0650.18220.07650.060.0352-0.0112-0.0127-0.0066-0.0221-0.005-0.070926.55491.27612.1827
67.8498-1.0099-1.64138.46373.52894.8814-0.01360.09910.0170.07890.3723-0.52670.34190.5033-0.3587-0.05640.0099-0.0162-0.04780.0534-0.082239.945-1.954920.182
721.19423.5427-9.55540.6538-2.1739.68571.1698-1.22771.46431.0468-0.69270.22450.4792-0.342-0.4771-0.08320.0613-0.0449-0.0602-0.04720.17122.68597.024914.0493
87.61141.0594-1.13844.1071-0.8910.3058-0.059-0.18340.23830.05730.07150.16560.02140.3192-0.0124-0.04050.003-0.0237-0.06280.0078-0.038113.93541.555712.1205
912.6138-1.14581.91374.59720.35940.35360.296-0.57110.1338-0.0056-0.27840.4695-0.3339-0.5853-0.0177-0.0343-0.0030.02050.08620.0804-0.00460.6769-5.167117.458
1018.21743.1834.75650.56050.94414.18450.0814-0.89840.21940.3948-0.2071-0.01950.231-0.29940.1257-0.0011-0.01270.0509-0.0686-0.0013-0.096126.5612-1.844526.5017
1115.3275.52784.089612.761.5891.33780.2628-0.1549-0.14450.1161-0.04380.104-0.16790.0962-0.2191-0.05110.01820.0293-0.05870.0199-0.163714.6925-10.090819.6378
126.64884.0966-4.14055.3755-9.341118.74710.1115-0.35040.24510.1727-0.229-0.51820.24460.29850.1175-0.1186-0.0144-0.0603-0.0320.0012-0.086239.08353.864720.9134
1312.675-1.37410.25510.021-4.772832.30480.10750.6425-0.1404-0.22950.1487-0.0995-0.44480.2504-0.2562-0.09290.01980.0985-0.1504-0.0214-0.052437.27974.65836.4503
143.53780.54631.11431.56910.37140.3778-0.0644-0.04760.2441-0.13690.0928-0.20770.08330.1843-0.0284-0.0112-0.0018-0.0288-0.0763-0.011-0.062436.12547.071612.773
1510.3546-4.49355.416110.4683-8.31527.00980.2025-0.0905-0.4315-0.02210.1070.21590.05790.1397-0.3094-0.0409-0.0336-0.0024-0.05290.00830.07051.8413-7.592512.6305
166.543410.0803-7.243728.2022-10.15038.09920.2781-0.39760.3853-0.4363-0.49380.578-0.13390.11060.2157-0.03650.0143-0.0994-0.00650.05290.06493.09335.98427.2375
173.43263.5425-0.03293.93610.83662.706-0.07810.4145-0.0208-0.24660.21860.3409-0.10990.1408-0.1405-0.0486-0.02760.0058-0.0260.00110.01554.4116-0.69326.9984
182.99382.09651.2952.5368-0.89523.599-0.0778-0.0775-0.15520.07830.0367-0.02560.1905-0.13960.0411-0.01590.02210.0089-0.02830.0153-0.075429.4827-3.969516.1196
196.57644.7293-5.58173.4337-3.89255.18820.2272-0.2890.26570.36450.00680.4317-0.42670.0384-0.234-0.00670.00240.0454-0.01030.00320.039910.8383-0.089218.7552
202.2979-0.7552-0.62134.67141.50684.41320.00780.05070.21750.1115-0.014-0.12460.0146-0.08240.0062-0.0226-0.0093-0.002-0.040.0194-0.078328.96749.19410.9977
210.0012-0.0140.04630.1581-0.52461.7410.00440.1682-0.2814-0.10090.2290.31630.148-0.2195-0.23340.0011-0.0288-0.060.03990.03010.022111.55910.41534.4554
226.85937.68033.83999.80494.63562.34870.0710.04260.0880.36050.11120.23810.26750.0473-0.1822-0.004-0.0361-0.00170.0177-0.00270.005719.9786-0.861817.21
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION1A94 - 99
3X-RAY DIFFRACTION1B1 - 5
4X-RAY DIFFRACTION1B94 - 99
5X-RAY DIFFRACTION2A6 - 10
6X-RAY DIFFRACTION3B6 - 10
7X-RAY DIFFRACTION4A11 - 20
8X-RAY DIFFRACTION5A21 - 32
9X-RAY DIFFRACTION6A33 - 43
10X-RAY DIFFRACTION7B11 - 20
11X-RAY DIFFRACTION8B21 - 32
12X-RAY DIFFRACTION9B33 - 43
13X-RAY DIFFRACTION10A44 - 56
14X-RAY DIFFRACTION11B44 - 56
15X-RAY DIFFRACTION12A57 - 62
16X-RAY DIFFRACTION13A63 - 68
17X-RAY DIFFRACTION14A69 - 76
18X-RAY DIFFRACTION15B57 - 62
19X-RAY DIFFRACTION16B63 - 68
20X-RAY DIFFRACTION17B69 - 76
21X-RAY DIFFRACTION18A77 - 85
22X-RAY DIFFRACTION19B77 - 85
23X-RAY DIFFRACTION20A86 - 93
24X-RAY DIFFRACTION21B86 - 93
25X-RAY DIFFRACTION22A200

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