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- PDB-6w6t: WT HIV-1 Protease in Complex with Phosphonated UMass6 (PU6) -

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Basic information

Entry
Database: PDB / ID: 6w6t
TitleWT HIV-1 Protease in Complex with Phosphonated UMass6 (PU6)
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV / PROTEASE / PROTEASE INHIBITOR / COMPLEX / HYDROLASE INHIBITOR COMPLEX / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


host multivesicular body / aspartic-type endopeptidase activity / virion membrane / 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: 1.84 Å
AuthorsLockbaum, G.J. / Henes, M. / Kosovrasti, K. / Nalivaika, E.A. / Ali, 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: To Be Published
Title: To Be Determined
Authors: Lockbaum, G.J. / Henes, M. / Kosovrasti, K. / Nalivaika, E.A. / Ali, A. / KurtYilmaz, N. / Schiffer, C.A.
History
DepositionMar 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 2.0Oct 18, 2023Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.formula / _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)22,6946
Polymers21,6642
Non-polymers1,0304
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-51 kcal/mol
Surface area9220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.130, 57.953, 61.694
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: 10831.833 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Details (production host): pXC35 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ULI9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TK7 / diethyl [(4-{(2S,3R)-4-{[(4-aminophenyl)sulfonyl](2-ethylbutyl)amino}-2-[({[(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl]oxy}carbonyl)amino]-3-hydroxybutyl}phenoxy)methyl]phosphonate


Mass: 741.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H52N3O11PS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 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: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.84→21.9 Å / Num. obs: 16226 / % possible obs: 98.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.7
Reflection shellResolution: 1.84→1.91 Å / Rmerge(I) obs: 0.29 / Num. unique obs: 1420

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Processing

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

6dgx


Resolution: 1.84→21.9 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.69
RfactorNum. reflection% reflection
Rfree0.2278 817 5.04 %
Rwork0.2003 --
obs0.2014 16208 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.84→21.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 65 167 1720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031579
X-RAY DIFFRACTIONf_angle_d0.6822152
X-RAY DIFFRACTIONf_dihedral_angle_d15.841915
X-RAY DIFFRACTIONf_chiral_restr0.051255
X-RAY DIFFRACTIONf_plane_restr0.004263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.95390.24311210.23142332X-RAY DIFFRACTION91
1.9539-2.10470.2571460.20162555X-RAY DIFFRACTION100
2.1047-2.31640.25451250.1962572X-RAY DIFFRACTION100
2.3164-2.65110.21941390.20562598X-RAY DIFFRACTION100
2.6511-3.33860.22741390.19492620X-RAY DIFFRACTION100
3.3386-21.90.21631470.19842714X-RAY DIFFRACTION99

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