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- PDB-7rq0: HIV Integrase CORE domain in complex with 2-{2-[2-(3-{[4-(2-{[(3-... -

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Basic information

Entry
Database: PDB / ID: 7rq0
TitleHIV Integrase CORE domain in complex with 2-{2-[2-(3-{[4-(2-{[(3-{2-[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}phenyl)methyl]amino}ethyl)piperazin-1-yl]methyl}phenyl)ethynyl]-5-methyl-1-benzofuran-3-yl}acetic acid
ComponentsIntegrase
KeywordsTRANSFERASE/INHIBITOR / HIV / Integrase / Inhibitor complex / 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-6I2 / IODIDE ION / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGorman, M.A. / Parker, M.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: HIV integrase-LEDGF interaction screening by fragment linking using off-rate screening
Authors: Gorman, M.A. / Parker, M.W.
History
DepositionAug 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 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

Downloads & links

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Assembly

Deposited unit
A: Integrase
B: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,62714
Polymers35,6832
Non-polymers1,94512
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-99 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.417, 46.417, 138.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Integrase


Mass: 17841.289 Da / Num. of mol.: 2 / Fragment: CORE domain (UNP residues 50-212)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q76353, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-6I2 / {2-[(3-{[4-(2-{[(3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}phenyl)methyl]amino}ethyl)piperazin-1-yl]methyl}phenyl)ethynyl]-5-methyl-1-benzofuran-3-yl}acetic acid


Mass: 733.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H43N3O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.09 Å3/Da / Density % sol: 41.08 % / Description: Bi-pyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.2 M ammonium sulfate, pH 7.0, 100 mM potassium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.95→46.42 Å / Num. obs: 41174 / % possible obs: 99.5 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 23.9
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 1409 / CC1/2: 0.869 / Rpim(I) all: 0.239

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3L3V

3l3v


Resolution: 1.95→38.54 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 30.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2703 4029 9.79 %
Rwork0.2298 --
obs0.2338 41174 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→38.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 0 90 59 2280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112251
X-RAY DIFFRACTIONf_angle_d2.0333042
X-RAY DIFFRACTIONf_dihedral_angle_d18.966299
X-RAY DIFFRACTIONf_chiral_restr0.063339
X-RAY DIFFRACTIONf_plane_restr0.009369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.4263840.32041083X-RAY DIFFRACTION83
1.98-20.271680.28241315X-RAY DIFFRACTION100
2-2.030.34311270.25991334X-RAY DIFFRACTION100
2.03-2.050.27581560.25931241X-RAY DIFFRACTION100
2.05-2.080.35741320.26391335X-RAY DIFFRACTION100
2.08-2.110.29511520.26381338X-RAY DIFFRACTION100
2.11-2.140.31061120.26451274X-RAY DIFFRACTION100
2.14-2.170.31491340.28651284X-RAY DIFFRACTION100
2.18-2.210.42961600.33951331X-RAY DIFFRACTION99
2.21-2.250.5311180.46041161X-RAY DIFFRACTION89
2.25-2.290.50591110.42391123X-RAY DIFFRACTION88
2.29-2.330.2771320.26891331X-RAY DIFFRACTION100
2.33-2.380.29311460.25431257X-RAY DIFFRACTION100
2.38-2.430.25191380.25051375X-RAY DIFFRACTION100
2.43-2.490.28681420.24571242X-RAY DIFFRACTION100
2.49-2.550.26151350.24521317X-RAY DIFFRACTION100
2.55-2.620.26641320.24321341X-RAY DIFFRACTION100
2.62-2.70.35161500.24631280X-RAY DIFFRACTION100
2.7-2.780.29071660.21721264X-RAY DIFFRACTION100
2.79-2.880.26221540.23291315X-RAY DIFFRACTION100
2.88-30.3027960.20771320X-RAY DIFFRACTION100
3-3.140.23331740.19821293X-RAY DIFFRACTION100
3.14-3.30.27121910.22311239X-RAY DIFFRACTION100
3.3-3.510.27341640.21461248X-RAY DIFFRACTION100
3.51-3.780.2361260.1891262X-RAY DIFFRACTION97
3.78-4.160.18061310.18921354X-RAY DIFFRACTION99
4.16-4.760.21311240.16561296X-RAY DIFFRACTION100
4.76-5.990.22381570.19321283X-RAY DIFFRACTION100
6-38.540.2421170.21931298X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 11.1595 Å / Origin y: 11.8569 Å / Origin z: -18.7156 Å
111213212223313233
T0.1868 Å20.0754 Å2-0.0083 Å2-0.1611 Å2-0.0164 Å2--0.1689 Å2
L1.9248 °20.8427 °20.1057 °2-1.5737 °20.0358 °2--3.8955 °2
S0.0666 Å °0.0517 Å °0.1166 Å °0.0346 Å °0.0308 Å °0.1099 Å °-0.0775 Å °-0.0873 Å °-0.0715 Å °
Refinement TLS groupSelection details: all

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