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- PDB-9eee: Room-temperature X-ray structure of HIV-1 protease in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9eee
TitleRoom-temperature X-ray structure of HIV-1 protease in complex with GRL-10624A inhibitor
ComponentsProtease
KeywordsHYDROLASE/INHIBITOR / HIV-1 protease / homodimer / inhibitor complex / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKovalevsky, A. / Gerlits, O. / Ghosh, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150466 United States
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2025
Title: Potent HIV‐1 protease inhibitors containing oxabicyclo octanol-derived P2-ligands: Design, synthesis, and X‐ray structural studies of inhibitor-HIV-1 protease complexes.
Authors: Ghosh, A.K. / Yadav, M. / Sharma, A. / Johnson, M. / Ghosh, A.K. / Prasad, R. / Amano, M. / Gerlits, O. / Kovalevsky, A. / Mitsuya, H.
History
DepositionNov 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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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)22,1695
Polymers21,4812
Non-polymers6883
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-37 kcal/mol
Surface area9570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.334, 60.013, 87.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Protease


Mass: 10740.677 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q5RZ08, HIV-1 retropepsin
#2: Chemical ChemComp-A1BHU / (3S,3aS,4S,7R,8aS)-3-methylhexahydro-1H,3H-3a,7-epoxycyclohepta[c]furan-4-yl {(2S,3R)-3-hydroxy-4-[(4-methoxybenzene-1-sulfonyl)(2-methylpropyl)amino]-1-phenylbutan-2-yl}carbamate


Mass: 616.765 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H44N2O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES, 0.7-1.0 M sodium chloride, pH 6.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→87.69 Å / Num. obs: 26844 / % possible obs: 97.1 % / Redundancy: 7 % / CC1/2: 0.981 / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.82
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.76 / Num. unique obs: 2618 / CC1/2: 0.585 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→24.72 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 1363 5.09 %random
Rwork0.171 ---
obs0.1725 26788 97.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→24.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 45 109 1666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071702
X-RAY DIFFRACTIONf_angle_d1.0062329
X-RAY DIFFRACTIONf_dihedral_angle_d13.942242
X-RAY DIFFRACTIONf_chiral_restr0.071275
X-RAY DIFFRACTIONf_plane_restr0.008283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.34441470.28862413X-RAY DIFFRACTION95
1.76-1.830.25891340.25592445X-RAY DIFFRACTION95
1.83-1.910.26381360.22632466X-RAY DIFFRACTION96
1.91-2.020.26391170.20242536X-RAY DIFFRACTION97
2.02-2.140.24721350.18492496X-RAY DIFFRACTION97
2.14-2.310.23731310.17572556X-RAY DIFFRACTION98
2.31-2.540.22071300.18612554X-RAY DIFFRACTION98
2.54-2.910.23471320.18442599X-RAY DIFFRACTION98
2.91-3.660.21241480.16112619X-RAY DIFFRACTION99
3.66-24.720.13671530.13662741X-RAY DIFFRACTION98

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