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- PDB-7le8: HIV-1 Protease WT (NL4-3) in Complex with PD4 (LR4-23) -

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Basic information

Entry
Database: PDB / ID: 7le8
TitleHIV-1 Protease WT (NL4-3) in Complex with PD4 (LR4-23)
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV / NL4-3 PROTEASE / 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 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.644 Å
AuthorsLockbaum, G.J. / Rusere, L.N. / Henes, M. / Kosovrasti, K. / Lee, S.K. / Spielvogel, E. / Nalivaika, E.A. / Swanstrom, R. / KurtYilmaz, N. / Schiffer, C.A. / Ali, 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: To Be Published
Title: HIV-1 Protease Inhibitors with a P1 Phosphonate Modification Maintain Potency against Drug Resistant Variants by Increased van der Waals Contacts with Flaps Residues
Authors: Lockbaum, G.J. / Rusere, L.N. / Henes, M. / Kosovrasti, K. / Lee, S.K. / Spielvogel, E. / Nalivaika, E.A. / Swanstrom, R. / KurtYilmaz, N. / Schiffer, C.A. / Ali, A.
History
DepositionJan 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4063
Polymers21,6642
Non-polymers7431
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-23 kcal/mol
Surface area9160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.260, 58.636, 61.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protease


Mass: 10831.833 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: Q8ULI9
#2: Chemical ChemComp-XUM / diethyl [(4-{(2S,3R)-4-{[(2H-1,3-benzodioxol-5-yl)sulfonyl](2-methylpropyl)amino}-2-[({[(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl]oxy}carbonyl)amino]-3-hydroxybutyl}phenoxy)methyl]phosphonate


Mass: 742.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H47N2O13PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.8 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.64→39.506 Å / Num. obs: 23234 / % possible obs: 99.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.7
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2194 / % possible all: 96.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.15.2_3472refinement
Cootmodel building
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DGX

6dgx


Resolution: 1.644→39.506 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 1167 5.03 %
Rwork0.1912 22032 -
obs0.1923 23199 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.21 Å2 / Biso mean: 35.1854 Å2 / Biso min: 15.13 Å2
Refinement stepCycle: final / Resolution: 1.644→39.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 0 97 128 1697
Biso mean--30.85 41.2 -
Num. residues----198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6442-1.7190.38651300.3355263797
1.719-1.80970.29391510.2612702100
1.8097-1.92310.26341440.22592721100
1.9231-2.07150.22631460.19252752100
2.0715-2.280.22011410.1852742100
2.28-2.60980.21941450.19332783100
2.6098-3.28790.22631520.1932789100
3.2879-39.5060.17921580.1733290699

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