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- PDB-3o9g: Crystal Structure of wild-type HIV-1 Protease in complex with af53 -

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Basic information

Entry
Database: PDB / ID: 3o9g
TitleCrystal Structure of wild-type HIV-1 Protease in complex with af53
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV-1 protease / drug resistance / drug design / Protease inhibitors / AIDS / Aspartyl protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


RNA stem-loop binding / host cell / 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 ...RNA stem-loop binding / host cell / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / endonuclease activity / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / 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 / 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-F53 / PHOSPHATE ION / Gag-Pol polyprotein / Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSchiffer, C.A. / Nalam, M.N.L.
CitationJournal: Chem.Biol. / Year: 2013
Title: Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance.
Authors: Nalam, M.N. / Ali, A. / Reddy, G.S. / Cao, H. / Anjum, S.G. / Altman, M.D. / Yilmaz, N.K. / Tidor, B. / Rana, T.M. / Schiffer, C.A.
History
DepositionAug 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Refinement description
Revision 1.2Nov 23, 2011Group: Structure summary
Revision 1.3Nov 27, 2013Group: Database references
Revision 1.4Mar 19, 2014Group: Other
Revision 1.5Nov 8, 2017Group: Refinement description / Category: software
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.7Apr 3, 2024Group: Refinement description / Category: 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)22,5076
Polymers21,6322
Non-polymers8764
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-36 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.675, 57.816, 61.741
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 /


Mass: 10815.790 Da / Num. of mol.: 2 / Fragment: HIV-1 protease (UNP residues 1 to 99) / Mutation: Q7K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: HXB2 / Gene: gag-pol, pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: Q90K99, UniProt: P03369*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-F53 / (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(1S,2R)-1-benzyl-3-[(2-ethylbutyl){[4-(hydroxymethyl)phenyl]sulfonyl}amino]-2-hydroxypropyl}carbamate


Mass: 590.728 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H42N2O8S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 295 K / Method: hanging drop, vapor diffusion / pH: 6.2
Details: 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 22322 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 16
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.65-1.715.40.371194.1
1.71-1.786.40.3151100
1.78-1.866.70.201199.9
1.86-1.966.70.1271100
1.96-2.086.80.0831100
2.08-2.246.80.0641100
2.24-2.466.90.0531100
2.46-2.826.90.0421100
2.82-3.556.90.0281100
3.55-506.50.022198.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry

Resolution: 1.65→42.22 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.501 / SU ML: 0.065 / SU R Cruickshank DPI: 0.1044 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20339 1142 5.1 %RANDOM
Rwork0.17594 ---
obs0.17738 21130 99.07 %-
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: 26.925 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2--0.32 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.65→42.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 56 136 1682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221636
X-RAY DIFFRACTIONr_bond_other_d0.0010.021088
X-RAY DIFFRACTIONr_angle_refined_deg1.4022.0192242
X-RAY DIFFRACTIONr_angle_other_deg0.84432690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0175210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.44825.08857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5115268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.12158
X-RAY DIFFRACTIONr_chiral_restr0.0950.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02293
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_it0.5811.51020
X-RAY DIFFRACTIONr_mcbond_other0.1721.5426
X-RAY DIFFRACTIONr_mcangle_it0.99521664
X-RAY DIFFRACTIONr_scbond_it1.623616
X-RAY DIFFRACTIONr_scangle_it2.4834.5578
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 72 -
Rwork0.261 1420 -
obs--90.86 %
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)
11.9378-0.8759-0.68152.39220.50391.9579-0.1756-0.16490.05420.32510.13230.01090.03240.15390.0432-0.01340.02420.0171-0.00540.0053-0.057720.76425.43729.629
22.9003-2.230.14331.8224-0.02442.7801-0.0437-0.0225-0.20470.1440.08270.19850.2889-0.0993-0.039-0.0125-0.00410.0259-0.050.0154-0.013219.6717.36223.15
31.61620.2340.22640.718-0.72620.8738-0.0002-0.0157-0.05240.0444-0.0431-0.019-0.061-0.00740.0433-0.02790.0066-0.0073-0.00410.0037-0.007327.67628.3819.103
43.57490.73760.32812.7533-0.36920.58610.0083-0.0281-0.0471-0.06180.02940.0785-0.0698-0.0559-0.0377-0.03290.004-0.0019-0.02460.0076-0.022412.42626.76518.764
54.0124-2.0828-1.97963.19311.84615.1773-0.0268-0.25950.01590.04390.0257-0.49320.10890.33290.0011-0.0521-0.019-0.0557-0.0150.02760.049239.58630.45624.199
610.146-3.7334-2.32161.40460.92710.7030.02370.0698-0.17310.0091-0.08830.03640.0064-0.15480.0647-0.0468-0.0146-0.00070.0153-0.00650.01170.88521.49917.948
72.332-0.17590.59953.38782.59484.5210.07240.10570.0563-0.0280.0824-0.281-0.12210.3187-0.1548-0.0645-0.01050.0046-0.0080.0330.005539.58931.6110.448
85.3593-0.6979-1.5943.67281.94582.91160.09290.1433-0.0514-0.0438-0.0850.35830.0461-0.4102-0.0079-0.04840.0113-0.00750.01540.0454-0.01980.39534.40213.494
96.7546-0.9356-0.67840.3579-0.03482.12780.00580.1329-0.0621-0.0529-0.00960.0214-0.02280.0550.0037-0.02490.01250.0082-0.02220.0064-0.012727.53230.9764.448
109.4839-1.9859-2.31691.6539-0.49731.34570.14770.07390.1139-0.0466-0.00910.0738-0.08070.0169-0.1386-0.02920.0051-0.0022-0.0156-0.0027-0.007912.41139.58911.667
111.3621.159-1.59453.8092-1.69243.1353-0.04750.11780.04290.02070.0440.1831-0.0979-0.02460.0035-0.039-0.0097-0.0207-0.01060.0203-0.009628.97533.34914.578
122.4591-1.29732.74122.4273-2.04683.33320.07120.1286-0.0506-0.08040.00190.10430.14730.1539-0.0731-0.03470.00920.0023-0.00910.0095-0.016910.43629.42612.272
132.05890.1375-0.70861.7012-1.32841.26660.0286-0.0326-0.06890.0625-0.0541-0.04880.06650.05350.0254-0.02530.0076-0.0042-0.0203-0.00550.009128.63119.39919.453
142.042-1.4334-1.65041.85660.16322.499-0.0057-0.2509-0.0128-0.0301-0.02230.1440.0268-0.04050.028-0.02960.01890.0060.02590.0011-0.009511.73528.65827.346
152.091-1.71893.25477.677-7.90059.42440.04340.1174-0.2695-0.4072-0.211-0.13190.10270.31720.1676-0.0660.03570.03580.01220.01220.012138.88823.31710.481
163.90593.9399-4.98834.5259-3.72519.4650.1809-0.10920.22740.22480.05210.2216-0.3412-0.0036-0.233-0.04190.04040.0017-0.01110.01980.03581.64536.54321.425
178.2892-2.894-1.64327.18212.16518.94950.1135-0.1130.35830.3469-0.0106-0.1638-0.39470.1963-0.1029-0.0685-0.0314-0.0605-0.06230.00610.01737.45724.12524.503
189.6954-4.01420.43784.89150.72754.1493-0.03160.2776-0.1195-0.1302-0.08480.02790.23120.09710.1164-0.03490.01050.0155-0.00410.0127-0.01922.59823.02224.275
191.8138-0.46451.20972.5168-1.98325.03980.05420.0397-0.06060.0176-0.1596-0.1847-0.00150.13840.1054-0.0584-0.0010.0087-0.05170.01170.011735.6721.81218.419
201.97580.8333-3.64525.7014-2.38586.8595-0.0254-0.04750.03390.23160.10480.3023-0.20350.0709-0.0794-0.09630.0239-0.0218-0.00490.0285-0.00944.01928.40825.551
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 DIFFRACTION2B1 - 5
5X-RAY DIFFRACTION2B94 - 99
6X-RAY DIFFRACTION2B6 - 10
7X-RAY DIFFRACTION3A20 - 32
8X-RAY DIFFRACTION4B20 - 32
9X-RAY DIFFRACTION5A11 - 19
10X-RAY DIFFRACTION6B11 - 19
11X-RAY DIFFRACTION7A33 - 43
12X-RAY DIFFRACTION8B33 - 43
13X-RAY DIFFRACTION9A44 - 57
14X-RAY DIFFRACTION10B44 - 57
15X-RAY DIFFRACTION11A77 - 85
16X-RAY DIFFRACTION12B77 - 85
17X-RAY DIFFRACTION13A86 - 93
18X-RAY DIFFRACTION14B86 - 93
19X-RAY DIFFRACTION15A58 - 62
20X-RAY DIFFRACTION16B58 - 62
21X-RAY DIFFRACTION17A63 - 68
22X-RAY DIFFRACTION18B63 - 68
23X-RAY DIFFRACTION19A69 - 76
24X-RAY DIFFRACTION20B69 - 76

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