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- PDB-9ctx: X-ray crystal structure of multi-drug resistant HIV-1 protease (P... -

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Basic information

Entry
Database: PDB / ID: 9ctx
TitleX-ray crystal structure of multi-drug resistant HIV-1 protease (P51) in complex with Darunavir
ComponentsProtease
KeywordsVIRAL PROTEIN / HIV-1 Protease
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsHayashi, H. / Yedidi, R. / Bulut, H. / Das, D. / Mitsuya, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Secondary amino-acid substitutions contribute to the emergence of HIV protease inhibitor resistance as directly as primary amino-acid substitutions.
Authors: Das, D. / Hayashi, H. / Yedidi, R.S. / Bulut, H. / Mitsuya, H.
History
DepositionJul 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5153
Polymers10,8761
Non-polymers6402
Water1,04558
1
A: Protease
hetero molecules

A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0316
Polymers21,7512
Non-polymers1,2804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area6220 Å2
ΔGint-41 kcal/mol
Surface area9190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.68, 62.68, 81.759
Angle α, β, γ (deg.)90, 90, 120
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-205-

HOH

21A-255-

HOH

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Components

#1: Protein Protease


Mass: 10875.717 Da / Num. of mol.: 1
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: O38893
#2: Chemical ChemComp-017 / (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE / Darunavir / TMC114 / UIC-94017


Mass: 547.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H37N3O7S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.15 M (NH3)2SO4, 0.1 M HEPES pH7.0, 20 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→45.22 Å / Num. obs: 14126 / % possible obs: 98.12 % / Redundancy: 19.5 % / CC1/2: 0.998 / Net I/σ(I): 9.9
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 565 / CC1/2: 0.59

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→45.22 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20793 705 -RANDOM
Rwork0.16464 ---
obs0.16688 13380 98.13 %-
Displacement parametersBiso mean: 21.327 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å2-0 Å2
2---0.13 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.55→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms764 0 44 58 866
LS refinement shellResolution: 1.55→1.58 Å /
Rfactor% reflection
Rfree0.326 -
Rwork0.289 -
obs-83.11 %

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