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- PDB-7uoq: CRYSTAL STRUCTURE OF HIV-1 INTEGRASE COMPLEXED WITH (2S)-2-(TERT-... -

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Basic information

Entry
Database: PDB / ID: 7uoq
TitleCRYSTAL STRUCTURE OF HIV-1 INTEGRASE COMPLEXED WITH (2S)-2-(TERT-BUTOXY)-2-(5-{2-[(2-CHLORO-6-M ETHYLPHENYL)METHYL]-1,2,3,4-TETRAHYDROISOQUINOLIN-6-YL}-4- (4,4-DIMETHYLPIPERIDIN-1-YL)-2-METHYLPYRIDIN-3-YL)ACETIC ACID
ComponentsIntegrase
KeywordsTRANSFERASE / INTEGRASE / HYDROLASE
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-O20 / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8867 Å
AuthorsLewis, H.A. / Muckelbauer, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Discovery and Preclinical Profiling of GSK3839919, a Potent HIV-1 Allosteric Integrase Inhibitor.
Authors: Parcella, K. / Wang, T. / Eastman, K. / Zhang, Z. / Yin, Z. / Patel, M. / Tu, Y. / Zheng, B.Z. / Walker, M.A. / Saulnier, M.G. / Frennesson, D. / Bowsher, M. / Gillis, E. / Peese, K. / ...Authors: Parcella, K. / Wang, T. / Eastman, K. / Zhang, Z. / Yin, Z. / Patel, M. / Tu, Y. / Zheng, B.Z. / Walker, M.A. / Saulnier, M.G. / Frennesson, D. / Bowsher, M. / Gillis, E. / Peese, K. / Belema, M. / Cianci, C. / Dicker, I.B. / McAuliffe, B. / Ding, B. / Falk, P. / Simmermacher, J. / Parker, D.D. / Sivaprakasam, P. / Kish, K. / Lewis, H. / Hanumegowda, U. / Jenkins, S. / Kadow, J.F. / Krystal, M. / Meanwell, N.A. / Naidu, B.N.
History
DepositionApr 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)20,5785
Polymers19,6851
Non-polymers8924
Water79344
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,15510
Polymers39,3712
Non-polymers1,7858
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4200 Å2
ΔGint-90 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.420, 71.420, 66.654
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Integrase


Mass: 19685.273 Da / Num. of mol.: 1 / Mutation: C56S, F139D, F185H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q76353
#2: Chemical ChemComp-O20 / (2S)-tert-butoxy[(5M)-5-{2-[(2-chloro-6-methylphenyl)methyl]-1,2,3,4-tetrahydroisoquinolin-6-yl}-4-(4,4-dimethylpiperidin-1-yl)-2-methylpyridin-3-yl]acetic acid


Mass: 604.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H46ClN3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.2-0.18M Ammonium Sulfate, 100mM Na acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98011 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 8, 2016 / Details: ???
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.8867→31.4815 Å / Num. obs: 15932 / % possible obs: 98.4 % / Redundancy: 4 % / Biso Wilson estimate: 34.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.022 / Rrim(I) all: 0.046 / Net I/σ(I): 18.2
Reflection shellResolution: 1.887→1.99 Å / Redundancy: 4 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2329 / % possible all: 99.5

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8867→31.4815 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2241 792 4.98 %
Rwork0.1803 15123 -
obs0.1825 15915 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.54 Å2 / Biso mean: 49.603 Å2 / Biso min: 19.99 Å2
Refinement stepCycle: final / Resolution: 1.8867→31.4815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1049 0 104 132 1285
Biso mean--50.93 60.01 -
Num. residues----140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131138
X-RAY DIFFRACTIONf_angle_d1.2071559
X-RAY DIFFRACTIONf_chiral_restr0.071172
X-RAY DIFFRACTIONf_plane_restr0.01217
X-RAY DIFFRACTIONf_dihedral_angle_d16.841660
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8867-2.00490.26581220.2286252199
2.0049-2.15960.20111390.18752513100
2.1596-2.37690.19981310.1722237694
2.3769-2.72070.2611330.1836253199
2.7207-3.42710.21351270.1922255999
3.4271-31.48150.22421400.1695262398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.99212.8794-5.44246.2333-2.31437.6459-0.16450.4971-0.4299-0.6265-0.0627-0.27920.2054-0.24090.29270.2956-0.00470.00120.2831-0.07150.222669.791152.407778.6751
24.0829-0.59960.42274.3418-0.18722.86370.16570.27040.0605-0.3453-0.2229-0.27010.28290.05070.05020.29580.02780.0190.2442-0.02250.234974.182356.853779.9694
38.2561-0.8833-3.3965.3211.93316.46380.14590.16150.04140.0141-0.1819-0.30440.04030.18120.03090.24430.0042-0.00710.18360.02940.19875.78652.749989.0548
42.9902-0.66-1.20563.09260.62283.91790.05470.1567-0.0784-0.1872-0.1613-0.54370.1055-0.2180.25410.2665-0.03950.01740.2509-0.00210.330167.152950.393485.532
54.2216-4.44440.53344.7971-0.93682.0472-0.20710.1135-0.4627-0.62010.12060.15320.17270.02350.09290.51650.03250.06440.3751-0.01740.343676.873640.886482.8059
68.3547-2.0279-2.91113.64410.35836.162-0.0471-0.0143-0.48040.141-0.14320.14850.853-0.12130.22050.371-0.02710.03970.21610.01410.224273.720944.105293.3097
71.5791-0.27040.65723.1582-2.89112.6908-0.33990.4346-0.9744-0.2752-0.57770.30310.7833-0.00720.69050.4828-0.0740.02330.3768-0.12080.452667.132843.128883.4359
86.18491.6766-0.067.3478-0.8365.4638-0.30250.7189-0.1396-1.4380.20530.2516-0.34730.04720.20210.49630.09850.05440.37860.00350.256175.18665.69371.8154
98.2859-0.2261-0.27514.3897-0.74514.57230.10890.1979-0.1261-0.3967-0.1842-0.0132-0.2452-0.03330.03220.27210.0275-0.00830.1718-0.0140.161871.789267.221778.6111
102.28442.8986-2.22295.4649-5.0915.0376-0.20540.8767-0.062-1.08870.00731.2015-0.1625-1.3717-0.22150.35110.1256-0.16280.6015-0.04230.592255.870167.181175.3512
119.0162-0.7557-0.90732.0864-1.51859.9047-0.34280.0802-0.43610.04630.46470.81360.1114-0.899-0.07020.26760.0222-0.0310.4289-0.0250.499254.415659.270884.9893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 57 THROUGH 68 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 69 THROUGH 93 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 94 THROUGH 105 )A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 106 THROUGH 117 )A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 118 THROUGH 123 )A0
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 124 THROUGH 133 )A0
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 134 THROUGH 149 )A0
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 150 THROUGH 171 )A0
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 172 THROUGH 185 )A0
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 186 THROUGH 195 )A0
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 196 THROUGH 208 )A0

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