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- PDB-3eky: Crystal Structure of wild-type HIV protease in complex with the i... -

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Basic information

Entry
Database: PDB / ID: 3eky
TitleCrystal Structure of wild-type HIV protease in complex with the inhibitor, Atazanavir
ComponentsProtease
KeywordsHYDROLASE / HIV protease / protease inhibitors / drug resistance / Atazanavir / AIDS / Protease
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / 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 / viral translational frameshifting / 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. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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. / 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-DR7 / PHOSPHATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchiffer, C.A. / Nalam, M.N.L.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: Extreme Entropy-Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease.
Authors: King, N.M. / Prabu-Jeyabalan, M. / Bandaranayake, R.M. / Nalam, M.N. / Nalivaika, E.A. / Ozen, A. / Yilmaz, N.K. / Schiffer, C.A.
History
DepositionSep 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 25, 2012Group: Database references
Revision 1.3Oct 17, 2012Group: Database references
Revision 1.4Oct 25, 2017Group: Refinement description / Category: software
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)22,7167
Polymers21,6322
Non-polymers1,0855
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-53 kcal/mol
Surface area9350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.862, 58.099, 61.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protease / Retropepsin / PR


Mass: 10815.790 Da / Num. of mol.: 2 / Fragment: UNP residues 491-589 / Mutation: Q7K,V64I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Strain: HXB2 / Gene: gag-pol / Plasmid: PXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: P03369, HIV-1 retropepsin
#2: Chemical ChemComp-DR7 / (3S,8S,9S,12S)-3,12-BIS(1,1-DIMETHYLETHYL)-8-HYDROXY-4,11-DIOXO-9-(PHENYLMETHYL)-6-[[4-(2-PYRIDINYL)PHENYL]METHYL]-2,5, 6,10,13-PENTAAZATETRADECANEDIOIC ACID DIMETHYL ESTER / ATAZANAVIR / METHYL [(1S,4S,5S,10S)-4-BENZYL-1,10-DI-TERT-BUTYL-5-HYDROXY-2,9,12-TRIOXO-7-(4-PYRIDIN-2-YLBENZYL)-13-OXA-3,7,8,11-TETRAAZATET RADEC-1-YL]CARBAMATE


Mass: 704.855 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H52N6O7 / Comment: medication, antiretroviral*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 126mM Sodium Phosphate pH 6.2; 63mM sodium citrate; 24-29% ammonium sulphate , 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 / 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: 1.8→50 Å / Num. obs: 16904 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 8.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F7A

1f7a


Resolution: 1.8→42.41 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.906 / SU ML: 0.083 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.147 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20857 861 5.1 %RANDOM
Rwork0.17566 ---
obs0.17739 16003 95.65 %-
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 mean: 17.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 71 201 1774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221615
X-RAY DIFFRACTIONr_bond_other_d0.0010.021550
X-RAY DIFFRACTIONr_angle_refined_deg1.1792.0332202
X-RAY DIFFRACTIONr_angle_other_deg0.70433596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8965200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03424.81554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55215272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.01158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021734
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02285
X-RAY DIFFRACTIONr_nbd_refined0.1810.2211
X-RAY DIFFRACTIONr_nbd_other0.1730.21537
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2740
X-RAY DIFFRACTIONr_nbtor_other0.0770.2984
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2121
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1630.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.225
X-RAY DIFFRACTIONr_mcbond_it0.4311.51066
X-RAY DIFFRACTIONr_mcbond_other0.1011.5416
X-RAY DIFFRACTIONr_mcangle_it0.59621610
X-RAY DIFFRACTIONr_scbond_it1.0263675
X-RAY DIFFRACTIONr_scangle_it1.534.5592
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 70 -
Rwork0.206 1158 -
obs--96.85 %
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)
12.2894-0.6437-0.38031.95050.59694.4295-0.05380.0066-0.11590.09680.04390.08270.2217-0.06030.0099-0.06830.00140.0122-0.10590.0105-0.055619.85817.851323.4417
20.51280.08420.4663.88720.17931.8766-0.0495-0.06560.02590.0957-0.0268-0.0109-0.0871-0.09280.0763-0.06020.0242-0.0025-0.0564-0.0207-0.090221.463326.195629.2668
34.89192.74621.19013.02381.14331.2569-0.03620.0659-0.0663-0.08650.02830.0359-0.03420.10180.0079-0.08350.0108-0.0078-0.06080.0206-0.075312.764326.750418.6597
44.64573.15690.99474.47221.84131.4944-0.00860.05730.06890.01690.00680.0881-0.0484-0.07230.0018-0.08690.0189-0.0076-0.0960.0294-0.069627.956528.239718.7934
518.9573-4.7085-3.0845.7262.0631.0928-0.1087-0.2715-0.2247-0.11430.01730.3826-0.0521-0.25520.0913-0.0968-0.0103-0.0222-0.03180.0005-0.07421.667821.240819.4203
64.81131.0559-3.44532.911-1.4993.3587-0.0889-0.2620.0603-0.0783-0.0827-0.25640.06930.31020.1716-0.0803-0.0009-0.0321-0.05850.0237-0.019339.425130.713123.4711
76.3001-0.7165-0.58384.85711.15163.6485-0.0136-0.0041-0.05420.0938-0.03450.34430.0707-0.11990.0481-0.1241-0.01940-0.05530.0413-0.06850.631634.262313.7629
85.716-0.3263-0.8581.01061.554.9148-0.02370.21330.19030.0063-0.0156-0.20840.03640.330.0393-0.11060.01850.0076-0.03130.0605-0.044539.701630.33429.4362
98.2741-0.1307-2.34351.7327-1.00972.4229-0.01150.1959-0.1161-0.0316-0.02690.06030.0777-0.0050.0384-0.07770.01750.0074-0.08770.0084-0.050912.621539.064811.2859
105.1208-1.91010.04991.0996-0.6721.8528-0.06480.03610.05060.04440.02530.01840.00460.07710.0394-0.06270.02160.0152-0.06570.0084-0.068827.083630.76314.5506
113.3568-3.63752.54724.4507-1.15496.99650.19860.32150.1425-0.1418-0.1766-0.08950.25050.2051-0.022-0.0862-0.01240.0132-0.05310.0212-0.055910.346228.974612.7385
123.09782.3177-0.27285.6823-0.60923.31230.0852-0.06730.36340.02230.04040.4746-0.1599-0.0325-0.1256-0.06880.0011-0.0038-0.09250.0244-0.031629.689432.788714.3447
134.7529-0.4019-3.63314.328-3.44856.0621-0.1344-0.1148-0.15030.21230.2460.30270.0162-0.1586-0.1115-0.05170.0101-0.0133-0.0193-0.0046-0.059212.129829.003727.1178
145.8361-1.82592.2580.6882-0.12433.7711-0.08180.1159-0.00520.00620.07740.05340.02970.06350.0044-0.0702-0.0073-0.0059-0.0648-0.0029-0.049829.095419.61619.7433
153.02034.5002-6.34057.8132-7.795515.77240.2244-0.20230.42370.15580.15080.2796-0.42-0.0395-0.3752-0.11870.0310.0025-0.05710.04780.04881.438236.392821.1021
162.1289-4.4644.24869.3744-8.482521.67440.37690.3948-0.1405-0.0216-0.51890.12130.43560.53830.142-0.1301-0.01140.0078-0.00040.0334-0.031739.11622.887610.2778
1719.328-20.43886.292233.8255-6.09432.07410.3470.5947-0.1758-0.2569-0.42380.06660.12610.28160.0768-0.03770.01340.0087-0.02050.018-0.13213.716223.674524.7927
1810.6622-1.2266-8.04621.58353.558317.79330.08220.12180.33620.25380.0316-0.1879-0.327-0.1045-0.1138-0.0848-0.0068-0.0106-0.12060.0087-0.031837.510524.281223.6439
192.15521.3827-2.21233.5197-1.93032.37010.02790.0760.05410.01650.15380.42450.0891-0.0316-0.1817-0.0531-0.0059-0.0232-0.04510.0182-0.05334.476229.722925.1099
202.2763-1.8016-0.33452.38351.62811.99040.0761-0.01750.0174-0.0554-0.0512-0.07760.46620.3063-0.0249-0.0895-0.0468-0.0097-0.05720.0096-0.06336.594321.644318.0526
218.0048-12.9789-9.533324.537917.303118.4333-0.0879-0.18040.0827-0.06650.0294-0.1556-0.27470.48490.0586-0.1278-0.0076-0.0223-0.07140.0398-0.0420.242731.452514.2111
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION1A94 - 99
3X-RAY DIFFRACTION1A6 - 10
4X-RAY DIFFRACTION2A1 - 5
5X-RAY DIFFRACTION2A94 - 99
6X-RAY DIFFRACTION2A6 - 10
7X-RAY DIFFRACTION3A20 - 32
8X-RAY DIFFRACTION4A20 - 32
9X-RAY DIFFRACTION5A11 - 20
10X-RAY DIFFRACTION6A11 - 20
11X-RAY DIFFRACTION7A33 - 43
12X-RAY DIFFRACTION8A33 - 43
13X-RAY DIFFRACTION9A44 - 57
14X-RAY DIFFRACTION10A44 - 57
15X-RAY DIFFRACTION11A77 - 85
16X-RAY DIFFRACTION12A77 - 85
17X-RAY DIFFRACTION13A86 - 93
18X-RAY DIFFRACTION14A86 - 93
19X-RAY DIFFRACTION15A57 - 62
20X-RAY DIFFRACTION16A57 - 62
21X-RAY DIFFRACTION17A63 - 68
22X-RAY DIFFRACTION18A63 - 68
23X-RAY DIFFRACTION19A69 - 76
24X-RAY DIFFRACTION20A69 - 76
25X-RAY DIFFRACTION21A1 - 100

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