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- PDB-7ke0: HIV-1 Integrase catalytic core domain complexed with allosteric i... -

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Basic information

Entry
Database: PDB / ID: 7ke0
TitleHIV-1 Integrase catalytic core domain complexed with allosteric inhibitor STP03-0404
ComponentsIntegrase
KeywordsTRANSFERASE/INHIBITOR / Integrase / inhibitor / HIV / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


DNA integration / RNA stem-loop binding / RNA-directed DNA polymerase activity / endonuclease activity / DNA recombination / symbiont entry into host cell / DNA binding / zinc ion binding
Similarity search - Function
Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Integrase core domain / Integrase, catalytic core ...Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Chem-WBV / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsLindenberger, J.J. / Kvaratskhelia, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI062520 United States
CitationJournal: Plos Pathog. / Year: 2021
Title: A highly potent and safe pyrrolopyridine-based allosteric HIV-1 integrase inhibitor targeting host LEDGF/p75-integrase interaction site.
Authors: Maehigashi, T. / Ahn, S. / Kim, U.I. / Lindenberger, J. / Oo, A. / Koneru, P.C. / Mahboubi, B. / Engelman, A.N. / Kvaratskhelia, M. / Kim, K. / Kim, B.
History
DepositionOct 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9392
Polymers18,4441
Non-polymers4951
Water52229
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8774
Polymers36,8872
Non-polymers9902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area3030 Å2
ΔGint-18 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.932, 71.932, 65.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

#1: Protein Integrase


Mass: 18443.689 Da / Num. of mol.: 1 / Mutation: F185H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: F2WR52, RNA-directed DNA polymerase
#2: Chemical ChemComp-WBV / (2S)-tert-butoxy{4-(4-chlorophenyl)-2,3,6-trimethyl-1-[(1-methyl-1H-pyrazol-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-5-yl}acetic acid / Pirmitegravir


Mass: 495.013 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H31ClN4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodiuim cacodylate trihydrate, 0.1 M ammonium sulfate, 10% PEG8000

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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: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.187→24 Å / Num. obs: 17510 / % possible obs: 99.7 % / Redundancy: 8.8 % / Biso Wilson estimate: 34.83 Å2 / Rpim(I) all: 0.034 / Rrim(I) all: 0.103 / Net I/σ(I): 22
Reflection shellResolution: 2.187→2.28 Å / Num. unique obs: 1029 / CC1/2: 0.918

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-30001.10.1_2155data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6EB2

6eb2


Resolution: 2.19→23.55 Å / SU ML: 0.3547 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.8475 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.269 1719 9.82 %
Rwork0.2503 15791 -
obs0.2522 17510 89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 2.19→23.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 35 29 1099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031093
X-RAY DIFFRACTIONf_angle_d0.65511489
X-RAY DIFFRACTIONf_chiral_restr0.0421164
X-RAY DIFFRACTIONf_plane_restr0.0021180
X-RAY DIFFRACTIONf_dihedral_angle_d3.5823618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.250.4053920.3036994X-RAY DIFFRACTION67.62
2.25-2.320.34611340.33081267X-RAY DIFFRACTION84.25
2.32-2.410.44551550.34611387X-RAY DIFFRACTION94.54
2.41-2.50.46671530.34011389X-RAY DIFFRACTION92.45
2.5-2.620.37961500.33651311X-RAY DIFFRACTION91.37
2.62-2.760.36961450.33971314X-RAY DIFFRACTION87.05
2.76-2.930.37771470.30761241X-RAY DIFFRACTION85.63
2.93-3.150.26771420.28551288X-RAY DIFFRACTION87.14
3.15-3.470.31831470.2631322X-RAY DIFFRACTION89.57
3.47-3.970.23431590.19951444X-RAY DIFFRACTION98.04
3.97-4.990.18091480.19131398X-RAY DIFFRACTION94.04
4.99-23.550.19251470.21411436X-RAY DIFFRACTION96.06

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