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- PDB-9obi: Room Temperature X-Ray Structure of HIV-1 Protease in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 9obi
TitleRoom Temperature X-Ray Structure of HIV-1 Protease in Complex with Inhibitor GRL-075-24A
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Aspartic protease / enzyme-inhibitor complex / HYDROLASE / HYDROLASE-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
AuthorsBhandari, D. / Kovalevsky, A. / Ghosh, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150466 United States
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Design, synthesis, evaluation and X-ray structural studies of potent HIV-1 protease inhibitors containing substituted oxaspirocyclic carbamates as the P2 ligands.
Authors: Ghosh, A.K. / Shaktah, R. / Ghosh, A.K. / Johnson, M.E. / Bhandari, D. / Amano, M. / Aoki, M. / Kovalevsky, A. / Mitsuya, H.
History
DepositionApr 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
C: Protease
D: Protease
E: Protease
F: Protease
G: Protease
H: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,77614
Polymers85,9258
Non-polymers2,8506
Water8,881493
1
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1763
Polymers21,4812
Non-polymers6951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-23 kcal/mol
Surface area9700 Å2
MethodPISA
2
C: Protease
D: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1763
Polymers21,4812
Non-polymers6951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-23 kcal/mol
Surface area9760 Å2
MethodPISA
3
E: Protease
F: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2124
Polymers21,4812
Non-polymers7302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-31 kcal/mol
Surface area9570 Å2
MethodPISA
4
G: Protease
H: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2124
Polymers21,4812
Non-polymers7302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-32 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.088, 69.487, 89.433
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protease


Mass: 10740.677 Da / Num. of mol.: 8
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-A1CAJ / (1S,5S,7S)-7-(2-methoxyphenyl)-8-oxaspiro[4.5]decan-1-yl {(2S,3R)-3-hydroxy-4-[(4-methoxybenzene-1-sulfonyl)(2-methylpropyl)amino]-1-phenylbutan-2-yl}carbamate


Mass: 694.877 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H50N2O8S / 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.: 493 / 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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES, pH 6.0, 0.7-1.0M NaCl

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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: Jan 9, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→89.43 Å / Num. obs: 91426 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.958 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.051 / Net I/σ(I): 14.37
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8892 / CC1/2: 0.713 / Rpim(I) all: 0.328 / % possible all: 96.8

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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→27.32 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 4565 5.01 %random
Rwork0.1681 ---
obs0.1696 91181 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→27.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6048 0 198 493 6739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086450
X-RAY DIFFRACTIONf_angle_d1.1078763
X-RAY DIFFRACTIONf_dihedral_angle_d8.785903
X-RAY DIFFRACTIONf_chiral_restr0.0751029
X-RAY DIFFRACTIONf_plane_restr0.0091076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.32531470.29142698X-RAY DIFFRACTION93
1.72-1.740.33221570.26252856X-RAY DIFFRACTION98
1.74-1.760.28581650.2382785X-RAY DIFFRACTION99
1.76-1.780.25511610.23272912X-RAY DIFFRACTION100
1.78-1.810.24661420.20832862X-RAY DIFFRACTION100
1.81-1.830.23071380.20462923X-RAY DIFFRACTION100
1.83-1.860.21661650.19812830X-RAY DIFFRACTION100
1.86-1.890.23771730.18282922X-RAY DIFFRACTION100
1.89-1.910.21321460.18332870X-RAY DIFFRACTION100
1.91-1.950.221620.18942915X-RAY DIFFRACTION100
1.95-1.980.22531480.19332857X-RAY DIFFRACTION100
1.98-2.020.22971550.16982868X-RAY DIFFRACTION100
2.02-2.050.21321570.16082884X-RAY DIFFRACTION100
2.05-2.10.19641440.15992932X-RAY DIFFRACTION100
2.1-2.140.20761310.15262874X-RAY DIFFRACTION100
2.14-2.190.17111260.1522935X-RAY DIFFRACTION100
2.19-2.250.21771130.15662957X-RAY DIFFRACTION100
2.25-2.310.2081250.16552913X-RAY DIFFRACTION100
2.31-2.370.21151520.17022893X-RAY DIFFRACTION100
2.37-2.450.23221640.1772902X-RAY DIFFRACTION100
2.45-2.540.19231810.1842887X-RAY DIFFRACTION100
2.54-2.640.21311630.17142909X-RAY DIFFRACTION100
2.64-2.760.24541620.17572894X-RAY DIFFRACTION100
2.76-2.910.18891330.17562931X-RAY DIFFRACTION100
2.91-3.090.1712010.16892865X-RAY DIFFRACTION100
3.09-3.330.20121720.15382913X-RAY DIFFRACTION100
3.33-3.660.17381150.14122957X-RAY DIFFRACTION100
3.66-4.190.14331570.13082927X-RAY DIFFRACTION100
4.19-5.270.11551660.11752948X-RAY DIFFRACTION100
5.27-27.320.27121440.22432797X-RAY DIFFRACTION93

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