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- PDB-6lmq: Crystal structure of HIV-1 integrase catalytic core domain in com... -

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Basic information

Entry
Database: PDB / ID: 6lmq
TitleCrystal structure of HIV-1 integrase catalytic core domain in complex with 2-(tert-butoxy)-2-[3-(3,4-dihydro-2H-1,4-benzoxazin-6-yl)-6-methanesulfonamido-2,3',4',5-tetramethyl-[1,1'-biphenyl]-4-yl]acetic acid
ComponentsIntegrase catalytic
KeywordsTRANSFERASE / hydrolase transferase/inhibitor
Function / homology
Function and homology information


HIV-1 retropepsin / 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 / viral penetration into host nucleus ...HIV-1 retropepsin / 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 / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
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 ...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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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
Similarity search - Domain/homology
Chem-940 / TRIETHYLENE GLYCOL / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSugiyama, S. / Iwaki, T. / Tamura, Y. / Tomita, K. / Matsuoka, E. / Arita, S. / Seki, T. / Yoshinaga, T. / Kawasuji, T.
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: Discovery of novel integrase-LEDGF/p75 allosteric inhibitors based on a benzene scaffold.
Authors: Sugiyama, S. / Iwaki, T. / Tamura, Y. / Tomita, K. / Matsuoka, E. / Arita, S. / Seki, T. / Yoshinaga, T. / Kawasuji, T.
History
DepositionDec 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrase catalytic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3445
Polymers18,4351
Non-polymers9094
Water48627
1
A: Integrase catalytic
hetero molecules

A: Integrase catalytic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,68710
Polymers36,8692
Non-polymers1,8188
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area5050 Å2
ΔGint-56 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.885, 71.885, 65.520
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 catalytic


Mass: 18434.723 Da / Num. of mol.: 1 / Mutation: F185K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
Production host: Escherichia coli (E. coli)
References: UniProt: P12497, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-940 / (2S)-2-[2-(3,4-dihydro-2H-1,4-benzoxazin-6-yl)-4-(3,4-dimethylphenyl)-3,6-dimethyl-5-(methylsulfonylamino)phenyl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid


Mass: 566.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H38N2O6S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium cacodylate pH6.5, 0.206M Ammonium sulfate, 1% PEG 8000, 5mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→62.25 Å / Num. obs: 11752 / % possible obs: 99.5 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.064 / Χ2: 1.411 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.1-2.144.60.5445800.939199.8
2.14-2.184.80.525721.015199.3
2.18-2.224.80.4415730.94199.8
2.22-2.264.90.3846021.0621100
2.26-2.314.90.3385640.978199.8
2.31-2.3750.3135741.069199.7
2.37-2.4250.2975831.0731100
2.42-2.4950.2355851.071100
2.49-2.565.10.195841.152199.8
2.56-2.655.10.1845831.2151100
2.65-2.745.10.1495781.2281100
2.74-2.855.20.1275901.392199.7
2.85-2.985.30.1045801.541199.7
2.98-3.145.20.0876011.621100
3.14-3.335.30.0745791.863199.8
3.33-3.595.40.0586041.9381100
3.59-3.955.30.0475892.017199.7
3.95-4.525.40.046062.037199.2
4.52-5.75.30.0366071.835199.5
5.7-504.90.0296181.793194.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.38 Å19.78 Å
Translation2.38 Å19.78 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREP10.2.31phasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LPT

3lpt


Resolution: 2.1→62.25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.362 / SU ML: 0.119 / SU R Cruickshank DPI: 0.1971 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.168
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 557 4.7 %RANDOM
Rwork0.2119 ---
obs0.2132 11184 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 96.52 Å2 / Biso mean: 41.278 Å2 / Biso min: 4.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.4 Å20 Å2
2--0.8 Å20 Å2
3----1.2 Å2
Refinement stepCycle: final / Resolution: 2.1→62.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1118 0 60 27 1205
Biso mean--42.46 41.23 -
Num. residues----143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221199
X-RAY DIFFRACTIONr_angle_refined_deg2.1111.9971626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4155140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89624.78346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.33615199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.385154
X-RAY DIFFRACTIONr_chiral_restr0.1590.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021856
LS refinement shellResolution: 2.1→2.153 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.37 36 -
Rwork0.292 812 -
obs--99.3 %

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