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- PDB-6mk9: X-ray crystal structure of darunavir-resistant-P51 HIV-1 protease... -

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Basic information

Entry
Database: PDB / ID: 6mk9
TitleX-ray crystal structure of darunavir-resistant-P51 HIV-1 protease in complex with GRL-121
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease-inhibitor complex / darunavir-resistance / P51 / GRL-121 / non-peptidic / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


host multivesicular body / aspartic-type endopeptidase activity / virion membrane / 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-7O7 / Protease / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYedidi, R.S. / Hayashi, H. / Das, D. / Mitsuya, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Citation
Journal: To Be Published
Title: X-ray crystal structure of darunavir-resistant-P51 HIV-1 protease in complex with GRL-121
Authors: Yedidi, R.S. / Hayashi, H. / Das, D. / Mitsuya, H.
#1: Journal: J. Virol. / Year: 2010
Title: In vitro selection of highly darunavir-resistant and replication-competent HIV-1 variants by using a mixture of clinical HIV-1 isolates resistant to multiple conventional protease inhibitors.
Authors: Koh, Y. / Amano, M. / Towata, T. / Danish, M. / Leshchenko-Yashchuk, S. / Das, D. / Nakayama, M. / Tojo, Y. / Ghosh, A.K. / Mitsuya, H.
History
DepositionSep 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
Revision 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num

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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)22,4223
Polymers21,7512
Non-polymers6711
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-23 kcal/mol
Surface area9380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.799, 62.799, 82.806
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: 10875.717 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: O38893, UniProt: A0A4P8EW36*PLUS
#2: Chemical ChemComp-7O7 / (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]-3-hydroxy-1-phenylbutan-2-yl}carbamate


Mass: 670.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H42N4O7S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.15 M Ammonium sulfate o.1 M HEPES pH6.8 15% (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 24079 / % possible obs: 99.3 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.05
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1177 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HLA

4hla


Resolution: 1.7→32.943 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.23 / Phase error: 19.82
RfactorNum. reflection% reflection
Rfree0.2044 1034 5.11 %
Rwork0.1662 --
obs0.1682 20242 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→32.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 46 212 1778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081693
X-RAY DIFFRACTIONf_angle_d1.0642320
X-RAY DIFFRACTIONf_dihedral_angle_d7.7481338
X-RAY DIFFRACTIONf_chiral_restr0.064270
X-RAY DIFFRACTIONf_plane_restr0.006284
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7002-1.78990.24691330.1942272799
1.7899-1.9020.19141520.171271999
1.902-2.04880.21271550.168270999
2.0488-2.2550.23331700.1657272799
2.255-2.58110.23121450.18252757100
2.5811-3.25150.21261530.17262761100
3.25150.16491260.1499280899

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