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- PDB-6dh2: Crystal structure of HIV-1 Protease NL4-3 I84V Mutant in complex ... -

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Basic information

Entry
Database: PDB / ID: 6dh2
TitleCrystal structure of HIV-1 Protease NL4-3 I84V Mutant in complex with UMass6
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV / Protease / NL4-3 / 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: 1.978 Å
AuthorsLockbaum, G.J. / Schiffer, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)NIH P01 GM109767 United States
CitationJournal: ACS Infect Dis / Year: 2019
Title: Structural Adaptation of Darunavir Analogues against Primary Mutations in HIV-1 Protease.
Authors: Lockbaum, G.J. / Leidner, F. / Rusere, L.N. / Henes, M. / Kosovrasti, K. / Nachum, G.S. / Nalivaika, E.A. / Ali, A. / Yilmaz, N.K. / Schiffer, C.A.
History
DepositionMay 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Protease
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3074
Polymers21,6362
Non-polymers6722
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-31 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.276, 57.826, 62.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protease


Mass: 10817.807 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A60 / (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-3-{[(4-aminophenyl)sulfonyl](2-ethylbutyl)amino}-1-benzyl-2-hydroxypropyl]carbamate


Mass: 575.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H41N3O7S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 23-24% (w/v) Ammonium Sulfate, 0.1M Bis-Tris-Methane-HCl Buffer pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.978→23.341 Å / Num. obs: 12775 / % possible obs: 95 % / Redundancy: 7.3 % / Net I/σ(I): 12.6
Reflection shellResolution: 1.978→2.1306 Å

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Processing

Software
NameVersionClassification
HKL-3000703xdata scaling
PHASERphasing
PHENIX1.12-2829refinement
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LL3

4ll3


Resolution: 1.978→23.341 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.61
RfactorNum. reflection% reflection
Rfree0.2342 636 4.99 %
Rwork0.1913 --
obs0.1935 12745 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.978→23.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 45 128 1657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041557
X-RAY DIFFRACTIONf_angle_d0.7572119
X-RAY DIFFRACTIONf_dihedral_angle_d15.618566
X-RAY DIFFRACTIONf_chiral_restr0.052253
X-RAY DIFFRACTIONf_plane_restr0.004262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9779-2.13060.24971210.19422280X-RAY DIFFRACTION92
2.1306-2.34480.27131310.19252354X-RAY DIFFRACTION94
2.3448-2.68370.2591230.20972397X-RAY DIFFRACTION95
2.6837-3.37950.25731210.20042462X-RAY DIFFRACTION96
3.3795-23.34220.20011400.17872616X-RAY DIFFRACTION98

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