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- PDB-6eb1: HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric I... -

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Basic information

Entry
Database: PDB / ID: 6eb1
TitleHIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor (2S)-tert-butoxy[3-(3,4-dihydro-2H-1-benzopyran-6-yl)-1-phenylisoquinolin-4-yl]acetic acid
ComponentsIntegrase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / HIV / Integrase / inhibitor / allosteric / TRANSFERASE-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
Ribonuclease H-like superfamily/Ribonuclease H / 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 ...Ribonuclease H-like superfamily/Ribonuclease H / 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. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-J3M / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLindenberger, J.J. / Kobe, M. / Kvaratskhelia, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI110310 United States
CitationJournal: ACS Med Chem Lett / Year: 2019
Title: An Isoquinoline Scaffold as a Novel Class of Allosteric HIV-1 Integrase Inhibitors.
Authors: Wilson, T.A. / Koneru, P.C. / Rebensburg, S.V. / Lindenberger, J.J. / Kobe, M.J. / Cockroft, N.T. / Adu-Ampratwum, D. / Larue, R.C. / Kvaratskhelia, M. / Fuchs, J.R.
History
DepositionAug 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8002
Polymers20,3331
Non-polymers4681
Water90150
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6014
Polymers40,6662
Non-polymers9352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area3030 Å2
ΔGint-14 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.338, 72.338, 66.619
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Integrase


Mass: 20332.787 Da / Num. of mol.: 1 / Fragment: catalytic core domain (UNP residues 50-212) / Mutation: F185H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F2WR52
#2: Chemical ChemComp-J3M / (2S)-tert-butoxy[3-(3,4-dihydro-2H-1-benzopyran-6-yl)-1-phenylisoquinolin-4-yl]acetic acid


Mass: 467.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C30H29NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M ammonium sulfate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 10% PEG8000, 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 19777 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rpim(I) all: 0.06 / Net I/σ(I): 19.9
Reflection shellResolution: 2.14→2.14 Å / Rpim(I) all: 0.315

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHENIXmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4O55

4o55


Resolution: 2.2→45.638 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.57
RfactorNum. reflection% reflection
Rfree0.2413 1744 10.09 %
Rwork0.2042 --
obs0.2081 17287 71.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→45.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 35 50 1145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091120
X-RAY DIFFRACTIONf_angle_d1.031523
X-RAY DIFFRACTIONf_dihedral_angle_d19.84633
X-RAY DIFFRACTIONf_chiral_restr0.052168
X-RAY DIFFRACTIONf_plane_restr0.004184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.26480.35711320.27211243X-RAY DIFFRACTION83
2.2648-2.33790.34781480.26451260X-RAY DIFFRACTION84
2.3379-2.42150.30521370.2561241X-RAY DIFFRACTION85
2.4215-2.51840.26821370.22481301X-RAY DIFFRACTION86
2.5184-2.6330.30321430.21761256X-RAY DIFFRACTION86
2.633-2.77180.22071530.21351287X-RAY DIFFRACTION87
2.7718-2.94550.25441460.211286X-RAY DIFFRACTION88
2.9455-3.17290.28951480.21131320X-RAY DIFFRACTION88
3.1729-3.4920.26761430.20281320X-RAY DIFFRACTION88
3.492-3.99710.17771520.17281306X-RAY DIFFRACTION89
3.9971-5.03490.18281510.16251348X-RAY DIFFRACTION90
5.0349-45.64740.22041540.20551375X-RAY DIFFRACTION93

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