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- PDB-7u2u: CRYSTAL STRUCTURE OF HIV-1 INTEGRASE COMPLEXED WITH Compound-2a A... -

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Basic information

Entry
Database: PDB / ID: 7u2u
TitleCRYSTAL STRUCTURE OF HIV-1 INTEGRASE COMPLEXED WITH Compound-2a AKA (2S)-2-(TERT-BUTOXY)-2-[7-(4,4-DIMETHYLPIPE RIDIN-1-YL)-8-{4-[2-(4-FLUOROPHENYL)ETHOXY]PHENYL}-2,5-DIM ETHYLIMIDAZO[1,2-A]PYRIDIN-6-YL]ACETIC ACID
ComponentsIntegrase
KeywordsDNA BINDING PROTEIN / viral protein / 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-KZD / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.839 Å
AuthorsKhan, J.A. / lewis, H. / Kish, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem. / Year: 2022
Title: Scaffold modifications to the 4-(4,4-dimethylpiperidinyl) 2,6-dimethylpyridinyl class of HIV-1 allosteric integrase inhibitors.
Authors: Parcella, K. / Patel, M. / Tu, Y. / Eastman, K. / Peese, K. / Gillis, E. / Belema, M. / Dicker, I.B. / McAuliffe, B. / Ding, B. / Falk, P. / Simmermacher, J. / Parker, D.D. / Sivaprakasam, P. ...Authors: Parcella, K. / Patel, M. / Tu, Y. / Eastman, K. / Peese, K. / Gillis, E. / Belema, M. / Dicker, I.B. / McAuliffe, B. / Ding, B. / Falk, P. / Simmermacher, J. / Parker, D.D. / Sivaprakasam, P. / Khan, J.A. / Kish, K. / Lewis, H. / Hanumegowda, U. / Jenkins, S. / Kadow, J.F. / Krystal, M. / Meanwell, N.A. / Naidu, B.N.
History
DepositionFeb 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Data collection / Source and taxonomy / Category: entity_src_gen / reflns_shell
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_redundancy / _reflns_shell.percent_possible_all
Revision 1.2Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5755
Polymers19,6851
Non-polymers8904
Water91951
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,15010
Polymers39,3712
Non-polymers1,7808
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area4250 Å2
ΔGint-90 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.421, 71.421, 67.130
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
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-KZD / (2S)-tert-butoxy[(4S)-7-(4,4-dimethylpiperidin-1-yl)-8-{4-[2-(4-fluorophenyl)ethoxy]phenyl}-2,5-dimethylimidazo[1,2-a]pyridin-6-yl]acetic acid


Mass: 601.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H44FN3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2-0.18M Ammonium Sulfate, 100mM Na acetate pH 4.6-5.0
PH range: 6.0?

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.839→61.85 Å / Num. obs: 17638 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 38.73 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.6

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (17-DEC-2019)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UM8

6um8


Resolution: 1.839→45.49 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.113 / SU Rfree Blow DPI: 0.1 / SU Rfree Cruickshank DPI: 0.099
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 849 4.82 %RANDOM
Rwork0.2029 ---
obs0.2033 17614 100 %-
Displacement parametersBiso max: 89.42 Å2 / Biso mean: 39.88 Å2 / Biso min: 25.08 Å2
Baniso -1Baniso -2Baniso -3
1--2.0727 Å20 Å20 Å2
2---2.0727 Å20 Å2
3---4.1454 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.839→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 59 51 1164
Biso mean--46.34 49.95 -
Num. residues----140
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d368SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes218HARMONIC5
X-RAY DIFFRACTIONt_it1134HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion152SEMIHARMONIC5
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_contact902SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1134HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg1551HARMONIC20.84
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion13.27
LS refinement shellResolution: 1.839→1.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 43
RfactorNum. reflection% reflection
Rfree0.2062 23 5.48 %
Rwork0.2064 397 -
all0.2064 420 -
obs--100 %

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