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- PDB-7le7: HIV-1 Protease WT (NL4-3) in Complex with GS-8374 -

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Basic information

Entry
Database: PDB / ID: 7le7
TitleHIV-1 Protease WT (NL4-3) in Complex with GS-8374
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 / MOLECULAR REPLACEMENT / Resolution: 1.978 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
B: Protease
A: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7777
Polymers21,6642
Non-polymers1,1135
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-71 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.420, 58.689, 62.009
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-KGQ / DIETHYL ({4-[(2S,3R)-2-({[(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YLOXY]CARBONYL}AMINO)-3-HYDROXY-4-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}BUTYL]PHENOXY}METHYL)PHOSPHONATE


Mass: 728.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C33H49N2O12PS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.16 Å3/Da / Density % sol: 43.04 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.978→24.2 Å / Num. obs: 13658 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 22.32 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 25.4
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 5 / Num. unique obs: 658 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHASERphasing
PHENIX1.12_2829refinement
Cootmodel building
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DGX

6dgx


Resolution: 1.978→24.191 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 688 5.05 %
Rwork0.1864 12929 -
obs0.1877 13617 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.1 Å2 / Biso mean: 29.8496 Å2 / Biso min: 10.25 Å2
Refinement stepCycle: final / Resolution: 1.978→24.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1485 0 118 178 1781
Biso mean--35.08 34.53 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021579
X-RAY DIFFRACTIONf_angle_d0.5992153
X-RAY DIFFRACTIONf_chiral_restr0.05255
X-RAY DIFFRACTIONf_plane_restr0.002262
X-RAY DIFFRACTIONf_dihedral_angle_d14.298911
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.978-2.13020.29361320.21372542
2.1302-2.34440.23511360.20092528
2.3444-2.68330.24191350.20412577
2.6833-3.37920.21261410.18762572
3.3792-24.1910.17351440.16882710

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