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- PDB-4o0j: HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric I... -

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Basic information

Entry
Database: PDB / ID: 4o0j
TitleHIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor (2S)-tert-butoxy[4-(4-chlorophenyl)-6-(3,4-dimethylphenyl)-2,5-dimethylpyridin-3-yl]ethanoic acid
ComponentsIntegrase
KeywordsVIRAL PROTEIN/INHIBITOR / HIV Integrase / CCD / DDE motif / allosteric inhibitor / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral ...Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / 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. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LF8 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsFeng, L. / Kvaratskhelia, M.
CitationJournal: Plos Pathog. / Year: 2014
Title: A New Class of Multimerization Selective Inhibitors of HIV-1 Integrase.
Authors: Sharma, A. / Slaughter, A. / Jena, N. / Feng, L. / Kessl, J.J. / Fadel, H.J. / Malani, N. / Male, F. / Wu, L. / Poeschla, E. / Bushman, F.D. / Fuchs, J.R. / Kvaratskhelia, M.
History
DepositionDec 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8935
Polymers18,1521
Non-polymers7404
Water95553
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,78510
Polymers36,3052
Non-polymers1,4808
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area4450 Å2
ΔGint-93 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.223, 72.223, 65.227
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: 18152.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12497
#2: Chemical ChemComp-LF8 / (2S)-tert-butoxy[4-(4-chlorophenyl)-6-(3,4-dimethylphenyl)-2,5-dimethylpyridin-3-yl]ethanoic acid


Mass: 451.985 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H30ClNO3
#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.: 53 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 277.5 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG8000, 0.1 M Na Cacodylate, pH 6.5, 0.1 M Ammonium Sulphate, Vapor Diffusion,hanging drop, temperature 277.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 25, 2013 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.04→62.55 Å / Num. all: 12903 / Num. obs: 12776 / % possible obs: 98.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.045 / Χ2: 1.869 / Net I/σ(I): 25.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.04-2.085.20.4776371.5191100
2.08-2.115.20.4136241.5041100
2.11-2.155.20.3286311.5281100
2.15-2.25.20.2836481.5771100
2.2-2.255.30.2426441.6381100
2.25-2.35.30.2056211.5911100
2.3-2.355.20.1756281.6271100
2.35-2.425.30.1676461.7561100
2.42-2.495.30.1386521.741100
2.49-2.575.30.1086211.831100
2.57-2.665.30.0996501.8381100
2.66-2.775.30.0816452.0241100
2.77-2.895.30.0666302.09199.8
2.89-3.055.30.0566532.179199.8
3.05-3.245.30.0476372.264199.2
3.24-3.495.30.0416402.281198.5
3.49-3.845.20.0346262.152195.9
3.84-4.395.10.0326202.147194.2
4.39-5.545.10.0286341.898195.1
5.54-504.90.0296892.177196

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å22.57 Å
Translation2.5 Å22.57 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.2.1phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→62.55 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.978 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 613 4.9 %RANDOM
Rwork0.1838 ---
all0.1845 12715 --
obs0.1861 12531 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.01 Å2 / Biso mean: 49.7556 Å2 / Biso min: 28.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.19 Å20 Å2
2--0.37 Å2-0 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.05→62.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 0 47 53 1200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191173
X-RAY DIFFRACTIONr_angle_refined_deg2.1181.9821584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0635137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40324.68147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.75815193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.62154
X-RAY DIFFRACTIONr_chiral_restr0.1540.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02840
X-RAY DIFFRACTIONr_mcbond_it4.5854.69563
X-RAY DIFFRACTIONr_mcangle_it6.4636.962692
X-RAY DIFFRACTIONr_scbond_it6.2255.089609
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 54 -
Rwork0.211 881 -
all-935 -
obs--99.36 %

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