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- PDB-5tys: X-ray crystal structure of wild type HIV-1 protease in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5tys
TitleX-ray crystal structure of wild type HIV-1 protease in complex with GRL-142
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / GRL-142 / HIV-1 PROTEASE / PROTEASE-INHIBITOR / DARUNAVIR / Pyran / Furan / NONPEPTIDIC / 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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-7OA / Protease / Pol protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.007 Å
AuthorsYedidi, R.S. / Hayashi, H. / Aoki, M. / Das, D. / Ghosh, A.K. / Mitsuya, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Elife / Year: 2017
Title: A novel central nervous system-penetrating protease inhibitor overcomes human immunodeficiency virus 1 resistance with unprecedented aM to pM potency.
Authors: Aoki, M. / Hayashi, H. / Rao, K.V. / Das, D. / Higashi-Kuwata, N. / Bulut, H. / Aoki-Ogata, H. / Takamatsu, Y. / Yedidi, R.S. / Davis, D.A. / Hattori, S.I. / Nishida, N. / Hasegawa, K. / ...Authors: Aoki, M. / Hayashi, H. / Rao, K.V. / Das, D. / Higashi-Kuwata, N. / Bulut, H. / Aoki-Ogata, H. / Takamatsu, Y. / Yedidi, R.S. / Davis, D.A. / Hattori, S.I. / Nishida, N. / Hasegawa, K. / Takamune, N. / Nyalapatla, P.R. / Osswald, H.L. / Jono, H. / Saito, H. / Yarchoan, R. / Misumi, S. / Ghosh, A.K. / Mitsuya, H.
History
DepositionNov 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3143
Polymers21,6082
Non-polymers7071
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-23 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.131, 63.131, 82.229
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protease /


Mass: 10803.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: C8B467, UniProt: G0X8E8*PLUS
#2: Chemical ChemComp-7OA / (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]carbamate


Mass: 706.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40F2N4O7S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1 M sodium/potassium phosphate (pH 6.2), 20% (w/v) polyethylene glycol 1000, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 12475 / % possible obs: 99.9 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 26.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.46 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HLA

4hla


Resolution: 2.007→32.86 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.71 / Phase error: 25.88
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 598 4.81 %Random
Rwork0.1949 ---
obs0.1969 12421 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.007→32.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 48 90 1654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081650
X-RAY DIFFRACTIONf_angle_d1.0222252
X-RAY DIFFRACTIONf_dihedral_angle_d10.557950
X-RAY DIFFRACTIONf_chiral_restr0.065266
X-RAY DIFFRACTIONf_plane_restr0.005268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0072-2.20920.26321610.1992290999
2.2092-2.52870.26631400.21142978100
2.5287-3.18550.24981460.21242947100
3.18550.21471510.18052989100

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