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- PDB-7l2y: HIV Integrase core domain in complex with inhibitor 2-(5-(3-fluor... -

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Basic information

Entry
Database: PDB / ID: 7l2y
TitleHIV Integrase core domain in complex with inhibitor 2-(5-(3-fluorophenyl)-2-(2-(thiophen-2-yl)ethynyl)-1- benzofuran-3-yl)ethanoic acid
ComponentsIntegrase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / HIV Integrase / 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 / 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
IODIDE ION / Chem-XHY / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.982 Å
AuthorsGorman, M.A. / Parker, M.W.
CitationJournal: To Be Published
Title: HIV Integrase core domain in complex with inhibitor
Authors: Gorman, M.A. / Parker, M.W.
History
DepositionDec 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,15911
Polymers17,8061
Non-polymers1,35310
Water75742
1
AAA: Integrase
hetero molecules

AAA: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,31822
Polymers35,6122
Non-polymers2,70620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5910 Å2
ΔGint-107 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.980, 45.980, 138.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Integrase


Mass: 17806.090 Da / Num. of mol.: 1 / Fragment: UNP residues 50-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: F2WR52
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / 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-XHY / 4-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzoic acid


Mass: 334.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H14O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.05 Å3/Da / Density % sol: 39.88 % / Description: Bi-pyramid
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 2.2 M ammonium sulfate, 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: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.98→32.62 Å / Num. obs: 11041 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 26.1 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.059 / Rrim(I) all: 0.159 / Χ2: 0.85 / Net I/σ(I): 9.6
Reflection shellResolution: 1.98→2.03 Å / Rmerge(I) obs: 1.322 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 758 / CC1/2: 0.731 / Rpim(I) all: 0.514

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.982→32.62 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.081 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.172
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2494 835 7.587 %
Rwork0.2092 10170 -
all0.212 --
obs-11005 99.665 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.879 Å2
Baniso -1Baniso -2Baniso -3
1-0.657 Å20 Å2-0 Å2
2--0.657 Å2-0 Å2
3----1.314 Å2
Refinement stepCycle: LAST / Resolution: 1.982→32.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1069 0 50 42 1161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131142
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171079
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.671551
X-RAY DIFFRACTIONr_angle_other_deg1.3571.5982484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5995141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93423.67349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44515191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.811154
X-RAY DIFFRACTIONr_chiral_restr0.0850.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021264
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02245
X-RAY DIFFRACTIONr_nbd_refined0.2250.2228
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.2983
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2536
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2560
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3260.247
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.229
X-RAY DIFFRACTIONr_nbd_other0.2470.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.29
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0290.21
X-RAY DIFFRACTIONr_mcbond_it2.9853.006558
X-RAY DIFFRACTIONr_mcbond_other2.9833557
X-RAY DIFFRACTIONr_mcangle_it4.3764.483695
X-RAY DIFFRACTIONr_mcangle_other4.3734.49696
X-RAY DIFFRACTIONr_scbond_it4.8293.648584
X-RAY DIFFRACTIONr_scbond_other4.6733.636581
X-RAY DIFFRACTIONr_scangle_it7.215.254854
X-RAY DIFFRACTIONr_scangle_other7.1015.228849
X-RAY DIFFRACTIONr_lrange_it9.37335.4271288
X-RAY DIFFRACTIONr_lrange_other9.3735.4271289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.982-2.0330.3570.251734X-RAY DIFFRACTION99.7478
2.033-2.0890.357660.244705X-RAY DIFFRACTION99.4839
2.089-2.1490.302510.236679X-RAY DIFFRACTION99.7268
2.149-2.2150.171500.196687X-RAY DIFFRACTION99.7294
2.215-2.2880.251500.189668X-RAY DIFFRACTION100
2.288-2.3680.201470.175628X-RAY DIFFRACTION99.8521
2.368-2.4570.268470.196611X-RAY DIFFRACTION99.697
2.457-2.5570.221490.199616X-RAY DIFFRACTION99.5509
2.557-2.670.301470.205557X-RAY DIFFRACTION100
2.67-2.80.266470.217541X-RAY DIFFRACTION99.8302
2.8-2.9510.297370.215539X-RAY DIFFRACTION99.8267
2.951-3.1290.252510.188489X-RAY DIFFRACTION100
3.129-3.3440.265490.221454X-RAY DIFFRACTION99.8016
3.344-3.610.219440.177444X-RAY DIFFRACTION100
3.61-3.9520.161280.178420X-RAY DIFFRACTION100
3.952-4.4140.169310.178374X-RAY DIFFRACTION99.7537
4.414-5.0880.201310.197343X-RAY DIFFRACTION100
5.088-6.210.266220.256282X-RAY DIFFRACTION97.7492
6.21-8.6950.35170.258248X-RAY DIFFRACTION99.6241

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