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- PDB-6w0u: HIV Integrase core domain in complex with inhibitor 2-(2-ethynyl-... -

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Basic information

Entry
Database: PDB / ID: 6w0u
TitleHIV Integrase core domain in complex with inhibitor 2-(2-ethynyl-5-methyl-1-benzofuran-3-yl)acetic acid
ComponentsIntegrase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / HIV Integrase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / endonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA 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. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
IODIDE ION / Chem-S0Y / Integrase / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.19 Å
AuthorsGorman, M.A. / Parker, M.W.
CitationJournal: To Be Published
Title: HIV Integrase core domain in complex with inhibitor
Authors: Gorman, M.A. / Parker, M.W.
History
DepositionMar 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release

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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)18,9948
Polymers18,0491
Non-polymers9457
Water46826
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,98916
Polymers36,0992
Non-polymers1,89014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4820 Å2
ΔGint-39 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.029, 46.029, 139.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Integrase /


Mass: 18049.484 Da / Num. of mol.: 1 / Fragment: core domain (UNP residues 50-212 / Mutation: Q53E,C56S,G124S,A125T,W131E,V151I,F185K,Q209E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: F2WR39, UniProt: P12497*PLUS
#2: Chemical ChemComp-S0Y / 2-(2-ethynyl-5-methyl-1-benzofuran-3-yl)ethanoic acid


Mass: 214.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.2 M ammonium sulfate, 100 mM potassium iodide

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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: Jan 27, 2015 / Details: AXCO Capillaries
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.19→43.71 Å / Num. obs: 8268 / % possible obs: 97.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 28.304 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.026 / Rrim(I) all: 0.059 / Χ2: 1.01 / Net I/σ(I): 27.6
Reflection shellResolution: 2.19→2.26 Å / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 622 / CC1/2: 0.883 / Rpim(I) all: 0.171 / Rrim(I) all: 0.341 / Χ2: 1.44

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.19→43.71 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.893 / SU B: 11.967 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.245 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26956 771 9.7 %RANDOM
Rwork0.21109 ---
obs0.21671 7175 96.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.108 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2--0.66 Å20 Å2
3----1.31 Å2
Refinement stepCycle: 1 / Resolution: 2.19→43.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 26 26 1114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131110
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181053
X-RAY DIFFRACTIONr_angle_refined_deg2.0871.6511502
X-RAY DIFFRACTIONr_angle_other_deg1.3941.5862438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4065138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.39723.40447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.36715191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.295154
X-RAY DIFFRACTIONr_chiral_restr0.0940.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021218
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02218
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3782.897555
X-RAY DIFFRACTIONr_mcbond_other2.3762.891554
X-RAY DIFFRACTIONr_mcangle_it3.8754.314692
X-RAY DIFFRACTIONr_mcangle_other3.8744.319693
X-RAY DIFFRACTIONr_scbond_it2.7753.268555
X-RAY DIFFRACTIONr_scbond_other2.7413.247552
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5424.702805
X-RAY DIFFRACTIONr_long_range_B_refined7.45733.541259
X-RAY DIFFRACTIONr_long_range_B_other7.43933.4821257
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.194→2.251 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 51 -
Rwork0.314 463 -
obs--89.55 %
Refinement TLS params.Method: refined / Origin x: 17.4662 Å / Origin y: 5.004 Å / Origin z: -3.9253 Å
111213212223313233
T0.0489 Å2-0.006 Å20.0039 Å2-0.0731 Å2-0.0194 Å2--0.0295 Å2
L0.5356 °2-0.3095 °2-0.0056 °2-0.2319 °20.1142 °2--1.3594 °2
S-0.0263 Å °0.0628 Å °-0.0596 Å °0.0166 Å °-0.0641 Å °0.069 Å °0.1093 Å °0.157 Å °0.0904 Å °

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