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- PDB-3oxv: Crystal Structure of HIV-1 I50V, A71 Protease in Complex with the... -

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Basic information

Entry
Database: PDB / ID: 3oxv
TitleCrystal Structure of HIV-1 I50V, A71 Protease in Complex with the protease inhibitor amprenavir.
ComponentsHIV-1 Protease
KeywordsHydrolase/Hydrolase Inhibitor / HIV-1 protease / inhibitor resistance / AIDS / Aspartyl protease / drug resistance / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA 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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / 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-478 / ACETATE ION / PHOSPHATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSchiffer, C.A. / Mittal, S. / Bandaranayake, R.M.
CitationJournal: J.Virol. / Year: 2013
Title: Structural and thermodynamic basis of amprenavir/darunavir and atazanavir resistance in HIV-1 protease with mutations at residue 50.
Authors: Mittal, S. / Bandaranayake, R.M. / King, N.M. / Prabu-Jeyabalan, M. / Nalam, M.N. / Nalivaika, E.A. / Yilmaz, N.K. / Schiffer, C.A.
History
DepositionSep 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: HIV-1 Protease
A: HIV-1 Protease
D: HIV-1 Protease
C: HIV-1 Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,42414
Polymers43,3194
Non-polymers2,10510
Water3,225179
1
B: HIV-1 Protease
A: HIV-1 Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8586
Polymers21,6602
Non-polymers1,1984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-23 kcal/mol
Surface area9220 Å2
MethodPISA
2
D: HIV-1 Protease
C: HIV-1 Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5668
Polymers21,6602
Non-polymers9076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-30 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.563, 63.338, 58.613
Angle α, β, γ (deg.)90.000, 96.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules BADC

#1: Protein
HIV-1 Protease / Retropepsin / PR


Mass: 10829.816 Da / Num. of mol.: 4 / Mutation: Q7K, I50V, A71V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: SF2 / Gene: gag-pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: P03369, HIV-1 retropepsin

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Non-polymers , 6 types, 189 molecules

#2: Chemical ChemComp-478 / {3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL-2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER / Amprenavir


Mass: 505.627 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H35N3O6S / Comment: protease inhibitor, medication*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 18-33% Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.03 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationMonochromator: Si (111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 36283 / % possible obs: 98 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.07 / Χ2: 1.002 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.814.20.44135650.954197
1.81-1.894.10.34935721.002197.1
1.89-1.974.10.23935971.003197.7
1.97-2.074.10.1736021.005197.8
2.07-2.24.10.13536281.001197.9
2.2-2.384.10.10836181.016198.1
2.38-2.614.10.08836441.011198.4
2.61-2.994.10.06336571.01198.7
2.99-3.7740.03936781.008198.9
3.77-503.90.02737221.013197.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F7A

1f7a


Resolution: 1.75→31.32 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 2.872 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 1809 5 %RANDOM
Rwork0.1686 ---
obs0.1705 36262 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 48.28 Å2 / Biso mean: 18.7927 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å2-0.38 Å2
2--0.38 Å20 Å2
3---0.54 Å2
Refine analyzeLuzzati coordinate error obs: 0.206 Å
Refinement stepCycle: LAST / Resolution: 1.75→31.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 0 140 179 3297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223266
X-RAY DIFFRACTIONr_bond_other_d0.0010.022181
X-RAY DIFFRACTIONr_angle_refined_deg1.362.0264467
X-RAY DIFFRACTIONr_angle_other_deg0.79335379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0755414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80124.815108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71815528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9831516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
X-RAY DIFFRACTIONr_mcbond_it0.8091.52028
X-RAY DIFFRACTIONr_mcbond_other0.2241.5846
X-RAY DIFFRACTIONr_mcangle_it1.46823307
X-RAY DIFFRACTIONr_scbond_it2.26231238
X-RAY DIFFRACTIONr_scangle_it3.6764.51160
LS refinement shellResolution: 1.75→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 121 -
Rwork0.204 2492 -
all-2613 -
obs--95.89 %
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)
12.9514-1.93552.5962.6571-0.33223.4108-0.3618-0.12790.2040.17940.155-0.1136-0.3417-0.06370.20680.11290.0186-0.02240.0866-0.01620.09636.015916.31710.1442
220.42111.33959.15270.15890.20175.58120.2554-0.0794-0.7628-0.00990.0856-0.05760.2772-0.3125-0.3410.1010.00530.01120.13820.00790.10025.50823.41613.1295
315.2197-0.76270.17534.73172.14031.73270.24610.69640.4676-0.2844-0.491-0.2071-0.0737-0.18990.24490.12740.01690.01920.1590.04560.14636.355116.2724-3.049
43.90051.20380.54211.0804-0.77561.17450.0612-0.011-0.1086-0.16380.0004-0.00670.20380.0236-0.06170.1007-0.01290.00890.1366-0.00050.07560.05157.46150.8817
56.982-0.72010.29282.3533-2.83697.42450.0038-0.2537-0.28780.0694-0.01090.07390.0518-0.30390.00720.1056-0.00860.01550.0593-0.01530.121-14.0631.1834-4.7634
60.56160.092-0.5452-0.0560.19333.50060.0204-0.0504-0.00270.0074-0.05330.02480.1331-0.12710.03290.10690.00780.02550.1437-0.00120.141711.06855.23163.4399
74.7469-0.8139-1.43947.1283-1.92511.7285-0.0238-0.05580.0286-0.05110.041-0.44880.04320.1126-0.01720.11150.0139-0.00290.1072-0.03180.092124.0763-2.7199-1.2102
820.0702-5.28755.72081.3906-1.40471.75840.15860.61790.1444-0.0962-0.1321-0.10420.00580.1075-0.02640.14090.01090.00370.1749-0.02980.1385-1.88490.9663-11.9732
94.9436-1.38170.06333.1707-0.41661.09740.0488-0.0011-0.221-0.0116-0.14290.0770.07040.00070.09410.1177-0.0074-0.01390.0844-0.01280.097911.9331-8.3486-0.8518
104.7242-2.0963-2.90479.2287.2735.99280.16290.24980.1221-0.3174-0.15960.0344-0.2617-0.1734-0.00330.09140.0255-0.02530.09930.00520.0883-12.87647.5127-7.5472
1116.32780.328410.60169.53942.164130.7380.2103-0.8209-0.38690.31260.0073-0.0840.3068-0.3586-0.21760.04760.00020.01630.07660.01190.0464-11.873612.1176.5729
121.2359-2.3739-1.58565.59246.046411.4711-0.034-0.0350.06130.10980.0604-0.081-0.0918-0.1766-0.02640.0853-0.00210.00520.0799-0.00280.0513-10.593913.39271.3008
133.50173.47323.22057.37286.25285.61190.2864-0.051-0.30190.0149-0.0297-0.2540.09490.0752-0.25670.09490.0262-0.00930.0990.01730.103523.3945-3.37284.759
1419.0702-13.72631.155523.3152-2.75248.62430.35960.28860.7508-0.3281-0.4362-0.1703-0.5253-0.06360.07660.1174-0.0420.01980.12940.02190.09923.616411.22026.0312
151.44010.05371.20981.4159-1.11123.55890.077-0.08910.05940.2754-0.03940.0448-0.17430.0642-0.03760.1414-0.00810.01670.1535-0.00120.128621.17785.50538.213
164.23031.46374.37612.17263.40216.15750.5287-0.0454-0.40150.2084-0.0764-0.18140.5517-0.0903-0.45230.1342-0.0427-0.03570.08520.0350.0897-3.91050.0803-0.5102
171.1182-0.03150.60963.7418-0.55452.26620.16890.1752-0.0919-0.3962-0.03260.07070.0864-0.127-0.13620.15180.0179-0.00210.1450.00030.104214.82962.3881-4.1322
184.5896-1.7884-0.43393.39680.52232.17-0.11950.0040.1397-0.0180.0584-0.10220.0564-0.05040.06110.0621-0.0177-0.01330.05230.00080.0709-2.454315.04350.843
193.5331-0.71.03381.48750.19072.7574-0.0349-0.10230.0519-0.089-0.1351-0.0339-0.0240.05050.170.0675-0.01080.01150.1066-0.0030.058813.94286.526410.5304
200000000000000000.0198000.019800.0198000
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 DIFFRACTION4A22 - 32
8X-RAY DIFFRACTION5A33 - 43
9X-RAY DIFFRACTION6B22 - 32
10X-RAY DIFFRACTION7B33 - 43
11X-RAY DIFFRACTION8A44 - 49
12X-RAY DIFFRACTION8A52 - 56
13X-RAY DIFFRACTION9B44 - 49
14X-RAY DIFFRACTION9B52 - 56
15X-RAY DIFFRACTION10A57 - 62
16X-RAY DIFFRACTION11A63 - 68
17X-RAY DIFFRACTION12A69 - 76
18X-RAY DIFFRACTION13B57 - 62
19X-RAY DIFFRACTION14B63 - 68
20X-RAY DIFFRACTION15B69 - 76
21X-RAY DIFFRACTION16A77 - 85
22X-RAY DIFFRACTION17B77 - 85
23X-RAY DIFFRACTION18A86 - 93
24X-RAY DIFFRACTION19B86 - 93
25X-RAY DIFFRACTION20C200

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