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- PDB-7t9h: HIV Integrase in complex with Compound-15 -

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Basic information

Entry
Database: PDB / ID: 7t9h
TitleHIV Integrase in complex with Compound-15
ComponentsIntegrase
KeywordsDNA BINDING PROTEIN / Viral protein / DNA Integration / AIDS / RNASEH / LEDGF / ENDONUCLEASE / HIV-1 integrase
Function / homology
Function and homology information


RNA stem-loop binding / DNA integration / 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
Chem-GE7 / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsKhan, J.A. / Lewis, H. / Kish, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Design, Synthesis, and Preclinical Profiling of GSK3739936 (BMS-986180), an Allosteric Inhibitor of HIV-1 Integrase with Broad-Spectrum Activity toward 124/125 Polymorphs.
Authors: Naidu, B.N. / Patel, M. / McAuliffe, B. / Ding, B. / Cianci, C. / Simmermacher, J. / Jenkins, S. / Parker, D.D. / Sivaprakasam, P. / Khan, J.A. / Kish, K. / Lewis, H. / Hanumegowda, U. / ...Authors: Naidu, B.N. / Patel, M. / McAuliffe, B. / Ding, B. / Cianci, C. / Simmermacher, J. / Jenkins, S. / Parker, D.D. / Sivaprakasam, P. / Khan, J.A. / Kish, K. / Lewis, H. / Hanumegowda, U. / Krystal, M. / Meanwell, N.A. / Kadow, J.F.
History
DepositionDec 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 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

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Assembly

Deposited unit
A: Integrase
B: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0196
Polymers36,2432
Non-polymers7764
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-28 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.885, 49.885, 226.385
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: 18121.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q76353
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GE7 / (2S)-tert-butoxy[2-methyl-4-(4-methylphenyl)quinolin-3-yl]acetic acid


Mass: 363.450 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H25NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 4.6%(w/v) PEG 3350, 261 mM ammonium acetate, 0.81% glycerol(v/v), 91 mM magnesium chloride and 100 mM MES pH 6.0
PH range: 6.0?

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 11604 / % possible obs: 98.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 68.56 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.6
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1119 / % possible all: 96.2

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (17-DEC-2019)refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NCJ

6ncj


Resolution: 2.53→34.34 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.885 / SU R Cruickshank DPI: 0.548 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.59 / SU Rfree Blow DPI: 0.306 / SU Rfree Cruickshank DPI: 0.306
RfactorNum. reflection% reflectionSelection details
Rfree0.2732 554 4.8 %RANDOM
Rwork0.2284 ---
obs0.2305 11536 98.7 %-
Displacement parametersBiso max: 124.99 Å2 / Biso mean: 72.43 Å2 / Biso min: 43.98 Å2
Baniso -1Baniso -2Baniso -3
1--11.9986 Å20 Å20 Å2
2---11.9986 Å20 Å2
3---23.9973 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.53→34.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 56 7 2255
Biso mean--64.04 52.24 -
Num. residues----296
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d736SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes390HARMONIC5
X-RAY DIFFRACTIONt_it2289HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion315SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1731SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2289HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3121HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion17.48
LS refinement shellResolution: 2.53→2.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 28
RfactorNum. reflection% reflection
Rfree0.2435 20 4.67 %
Rwork0.2982 408 -
all0.2949 428 -
obs--95.01 %
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)
14.7874-0.52610.22122.8462-0.29156.7252-0.2948-0.47770.16310.09040.1458-0.1746-0.73230.12840.149-0.19190.1634-0.00540.19730.0431-0.263913.2073-18.7837-24.2932
24.0675-0.7475-0.30611.4665-1.3016.7664-0.2773-0.48860.02510.31220.22350.2126-0.0508-0.41880.0539-0.19250.25750.03820.21220.0971-0.22680.2397-27.5918-11.6742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A53 - 209
2X-RAY DIFFRACTION2{ B|* }B57 - 208

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