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- PDB-4yoa: Crsystal structure HIV-1 Protease MDR769 L33F Complexed with darunavir -

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Basic information

Entry
Database: PDB / ID: 4yoa
TitleCrsystal structure HIV-1 Protease MDR769 L33F Complexed with darunavir
ComponentsHIV-1 Protease
KeywordsHydrolase/Hydrolase inhibitor / HIV-1 Protease / complex / darunavir / 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
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.697 Å
AuthorsKuiper, B.D. / Keusch, B. / Dewdney, T.G. / Chordia, P. / Brunzelle, J.S. / Ross, K. / Kovari, I.A. / MacArthur, R. / Salimnia, H. / Kovari, L.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Biochem Biophys Rep / Year: 2015
Title: The L33F darunavir resistance mutation acts as a molecular anchor reducing the flexibility of the HIV-1 protease 30s and 80s loops.
Authors: Kuiper, B.D. / Keusch, B.J. / Dewdney, T.G. / Chordia, P. / Ross, K. / Brunzelle, J.S. / Kovari, I.A. / MacArthur, R. / Salimnia, H. / Kovari, L.C.
History
DepositionMar 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3522
Polymers10,8051
Non-polymers5481
Water1,27971
1
A: HIV-1 Protease
hetero molecules

A: HIV-1 Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7054
Polymers21,6092
Non-polymers1,0952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4940 Å2
ΔGint-34 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.470, 45.470, 102.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HIV-1 Protease


Mass: 10804.702 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: Q5RTL1
#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 / Comment: medication, antiretroviral*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.45 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2.4M ammonium sulfate, 0.1 M MES, pH 6.2; 2.4M ammonium sulfate, 0.1 M MES, pH 6.2

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.697→102.22 Å / Num. obs: 12545 / % possible obs: 99.9 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 26.9
Reflection shellResolution: 1.7→1.9 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YOB
Resolution: 1.697→27.267 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 1248 10 %
Rwork0.1901 --
obs0.1937 12478 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.697→27.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 0 38 71 869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014844
X-RAY DIFFRACTIONf_angle_d1.5431156
X-RAY DIFFRACTIONf_dihedral_angle_d18.075326
X-RAY DIFFRACTIONf_chiral_restr0.079138
X-RAY DIFFRACTIONf_plane_restr0.006144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6974-1.76540.29651330.25721201X-RAY DIFFRACTION100
1.7654-1.84570.33711360.23221220X-RAY DIFFRACTION100
1.8457-1.9430.261360.21011218X-RAY DIFFRACTION100
1.943-2.06470.26781360.20691230X-RAY DIFFRACTION100
2.0647-2.2240.26371350.19651222X-RAY DIFFRACTION100
2.224-2.44770.23741390.19391249X-RAY DIFFRACTION100
2.4477-2.80160.21751390.20071257X-RAY DIFFRACTION100
2.8016-3.52850.21541430.1881275X-RAY DIFFRACTION100
3.5285-27.27060.20381510.17511358X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -2.5067 Å / Origin y: 4.1052 Å / Origin z: -14.1033 Å
111213212223313233
T0.2071 Å2-0.0443 Å20.0518 Å2-0.2082 Å20.0018 Å2--0.2117 Å2
L1.1087 °2-0.3277 °20.1024 °2-1.1569 °21.2848 °2--2.651 °2
S0.0755 Å °-0.1128 Å °0.112 Å °0.1188 Å °-0.0595 Å °0.0093 Å °0.2009 Å °-0.1883 Å °-0.0014 Å °
Refinement TLS groupSelection details: (chain A and resseq 1:99)

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