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- PDB-3ekq: Crystal structure of inhibitor saquinavir (SQV) in complex with m... -

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Entry
Database: PDB / ID: 3ekq
TitleCrystal structure of inhibitor saquinavir (SQV) in complex with multi-drug resistant HIV-1 protease (L63P/V82T/I84V) (referred to as ACT in paper)
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease inhibitor / drug resistance / entropy enthalpy compensation / AIDS / Hydrolase-hydrolase inhibitor complex / 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 penetration into host nucleus ...: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral penetration into host nucleus / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 / host cell plasma membrane / virion membrane / structural molecule activity / 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. / 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
Saquinavir / PHOSPHATE ION / Chem-ROC / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHIV-1 M:B_ARV2/SF2 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsPrabu-Jeyabalan, M. / King, N.M. / Schiffer, C.A. / Nalivaika, E.
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: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 25, 2012Group: Database references
Revision 1.3Oct 17, 2012Group: Database references
Revision 1.4Feb 27, 2013Group: Other
Revision 1.5Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.6Oct 20, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / 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 1.7Aug 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)22,5525
Polymers21,6922
Non-polymers8613
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-26 kcal/mol
Surface area8950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.164, 59.291, 61.389
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsOne dimer (A & B identifiers) in one asymmetric unit

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Components

#1: Protein Protease / / Retropepsin / PR


Mass: 10845.814 Da / Num. of mol.: 2 / Fragment: UNP residues 491-589 / Mutation: Q7K, L10I, G48V, I54V, V64I, V82T
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-ROC / (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide / / Fortovase / SAQUINAVIR / RO 31-8959 / Saquinavir


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 670.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H50N6O5 / References: Saquinavir / Comment: medication, antiretroviral*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR ROC IS A HYDROXYETHYLAMINE CONTAINING TRANSITION STATE MIMETIC.

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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: 42.69 %
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: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 28, 2008 / 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→42 Å / Num. all: 12975 / Num. obs: 12975 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 6

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Processing

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

1f7a


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0 / SU B: 9.298 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.334 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 467 4.8 %RANDOM
Rwork0.195 ---
obs0.197 9751 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.39 Å2 / Biso mean: 34.606 Å2 / Biso min: 17.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2---1.19 Å20 Å2
3---2.33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 0 59 74 1610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221583
X-RAY DIFFRACTIONr_bond_other_d0.0050.021523
X-RAY DIFFRACTIONr_angle_refined_deg1.2732.0152170
X-RAY DIFFRACTIONr_angle_other_deg0.71433527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9535200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.44125.09851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59315246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.06156
X-RAY DIFFRACTIONr_chiral_restr0.0770.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021723
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02285
X-RAY DIFFRACTIONr_nbd_refined0.1790.2208
X-RAY DIFFRACTIONr_nbd_other0.2050.21478
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2719
X-RAY DIFFRACTIONr_nbtor_other0.0870.2888
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.264
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0320.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1470.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0720.22
X-RAY DIFFRACTIONr_mcbond_it1.0631.51276
X-RAY DIFFRACTIONr_mcbond_other0.1241.5414
X-RAY DIFFRACTIONr_mcangle_it1.02221610
X-RAY DIFFRACTIONr_scbond_it1.663704
X-RAY DIFFRACTIONr_scangle_it2.2124.5560
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 30 -
Rwork0.226 594 -
all-624 -
obs--88.01 %
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)
14.2752.70270.09997.51490.05820.4083-0.14260.47320.4162-0.63320.13850.2435-0.0172-0.250.00410.0031-0.0802-0.06450.00520.0314-0.097220.22728.96362.5108
212.2035-3.3844-1.7161.93510.00260.4661-0.3962-0.56790.27450.01460.4136-0.2390.18190.0818-0.0174-0.0144-0.01780.0087-0.0315-0.0242-0.032928.60789.492212.1298
35.62083.9950.46074.9133-0.62870.4786-0.4040.7706-0.2739-0.17030.07430.57120.6178-0.38410.3297-0.0746-0.0544-0.03960.0677-0.0622-0.091411.968-0.32454.8674
429.374910.62336.484211.83911.76621.47320.4616-1.27470.06340.7436-0.55520.37590.2606-0.45650.0936-0.0306-0.0220.022-0.0166-0.0111-0.122125.8005-1.004726.3472
55.90512.53661.19915.97361.44231.5150.1515-0.1992-0.00030.51430.02010.5660.17580.1678-0.1716-0.1038-0.0132-0.0092-0.09950.01650.099715.2521-10.578519.498
63.0926-1.56780.48093.572-0.02340.09230.0157-0.1459-0.0576-0.1341-0.10820.04220.4332-0.03420.0925-0.0365-0.0016-0.007-0.04680.0110.019929.8621-3.783416.4627
76.873-2.57311.021613.07353.17541.19710.2038-0.7587-0.39511.74550.05160.82-0.70890.1804-0.25540.0227-0.07250.0208-0.03290.08380.032510.54780.082918.9099
87.1636-0.2318-0.62865.1256-1.00330.25990.0024-0.1041-0.17850.0514-0.0220.2198-0.04430.18940.0196-0.0681-0.0066-0.0096-0.0146-0.02150.0225.14944.249513.2486
910.0186-2.43331.19275.1849-0.42740.1461-0.2772-0.054-0.1564-0.2057-0.0564-0.04840.0836-0.03020.3336-0.04420.0104-0.0115-0.0238-0.0614-0.055115.30810.411110.2496
1020.5527-3.1504-0.226813.4555-2.11770.3596-0.2209-0.9087-0.75910.48870.4670.8363-0.50220.353-0.24610.0603-0.0297-0.0120.06640.09220.120319.8884-0.590318.0082
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION1B1 - 5
3X-RAY DIFFRACTION1A94 - 99
4X-RAY DIFFRACTION1B94 - 99
5X-RAY DIFFRACTION2A86 - 92
6X-RAY DIFFRACTION3B86 - 92
7X-RAY DIFFRACTION4A44 - 55
8X-RAY DIFFRACTION5B44 - 55
9X-RAY DIFFRACTION6A77 - 85
10X-RAY DIFFRACTION7B77 - 85
11X-RAY DIFFRACTION8A24 - 31
12X-RAY DIFFRACTION9B24 - 31
13X-RAY DIFFRACTION10A100

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