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- PDB-6opx: HIV-1 Protease NL4-3 I13V, G16E, V32I, L33F, K45I, M46I, L76V, V8... -

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Basic information

Entry
Database: PDB / ID: 6opx
TitleHIV-1 Protease NL4-3 I13V, G16E, V32I, L33F, K45I, M46I, L76V, V82F, I84V Mutant in complex with darunavir
ComponentsProtease NL4-3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV / NL4-3 PROTEASE / DRUG RESISTANCE / PROTEASE INHIBITOR / HYDROLASE 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsLockbaum, G.J. / Henes, M. / Kosovrasti, K. / Leidner, F. / Nachum, G.S. / Nalivaika, E.A. / Bolon, D.N.A. / KurtYilmaz, N. / Schiffer, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01-GM109767 United States
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance.
Authors: Henes, M. / Lockbaum, G.J. / Kosovrasti, K. / Leidner, F. / Nachum, G.S. / Nalivaika, E.A. / Lee, S.K. / Spielvogel, E. / Zhou, S. / Swanstrom, R. / Bolon, D.N.A. / Kurt Yilmaz, N. / Schiffer, C.A.
History
DepositionApr 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
B: Protease NL4-3
A: Protease NL4-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3953
Polymers21,8482
Non-polymers5481
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-32 kcal/mol
Surface area8940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.885, 61.885, 81.509
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 NL4-3


Mass: 10923.841 Da / Num. of mol.: 2
Mutation: Q7QK, I13V, G16E, V32I, L33F, K45I, M46I, L76V, V82F, I84V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7ZCI0
#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, antiretroviral*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 19-26% (w/v) Ammonium Sulfate, 0.1M Bis-Tris-Methane-HCl Buffer pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 11470 / % possible obs: 99.5 % / Redundancy: 11.1 % / Net I/σ(I): 33.8
Reflection shellResolution: 2.032→2.2359 Å / Num. unique obs: 2817

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Processing

Software
NameVersionClassification
HKL-3000v703xdata scaling
PHASERphasing
PHENIX1.12-2829refinement
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DH0

6dh0


Resolution: 2.03→22.39 Å / Cross valid method: FREE R-VALUE / σ(F): 7.3 / Phase error: 31.55
RfactorNum. reflection% reflection
Rfree0.2563 561 4.9 %
Rwork0.2314 --
obs0.2478 11446 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.03→22.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 38 110 1658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031581
X-RAY DIFFRACTIONf_angle_d0.6782156
X-RAY DIFFRACTIONf_dihedral_angle_d17.654915
X-RAY DIFFRACTIONf_chiral_restr0.052257
X-RAY DIFFRACTIONf_plane_restr0.003269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0317-2.23590.31111450.30642672X-RAY DIFFRACTION94
2.2359-2.55860.35561440.30682706X-RAY DIFFRACTION94
2.5586-3.22050.30111380.26092710X-RAY DIFFRACTION95
3.2205-17.86530.22551340.20762751X-RAY DIFFRACTION95

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