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- PDB-6w42: HIV Integrase core domain in complex with inhibitor 2-(5-methyl-2... -

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Basic information

Entry
Database: PDB / ID: 6w42
TitleHIV Integrase core domain in complex with inhibitor 2-(5-methyl-2-(2-(thiophen-2-yl)ethynyl)-1-benzofuran-3-yl)acetic acid
ComponentsHIV Integrase catalytic domain
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / HIV Integrase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homologyIODIDE ION / Chem-SJY
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.26 Å
AuthorsGorman, M.A. / Parker, M.W.
CitationJournal: To Be Published
Title: HIV Integrase core domain in complex with inhibitor (5-methyl-1-benzofuran-3-yl)acetic acid
Authors: Gorman, M.A. / Parker, M.W.
History
DepositionMar 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV Integrase catalytic domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0018
Polymers18,0051
Non-polymers9967
Water45025
1
A: HIV Integrase catalytic domain
hetero molecules

A: HIV Integrase catalytic domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,00316
Polymers36,0112
Non-polymers1,99214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4820 Å2
ΔGint-61 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.180, 46.180, 139.430
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 HIV Integrase catalytic domain


Mass: 18005.365 Da / Num. of mol.: 1 / Mutation: Q53E,C56S,G124S,A125T,W131E,V151I,F185K,Q209E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: RNA-directed DNA polymerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-SJY / 2-[5-methyl-2-(2-thiophen-2-ylethynyl)-1-benzofuran-3-yl]ethanoic acid


Mass: 296.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.06 Å3/Da / Density % sol: 40.22 %
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: Mar 24, 2015 / Details: AXCO Capillary optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→32.76 Å / Num. obs: 7718 / % possible obs: 100 % / Redundancy: 4.4 % / Biso Wilson estimate: 32.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.027 / Rrim(I) all: 0.057 / Χ2: 0.75 / Net I/σ(I): 15.3
Reflection shellResolution: 2.26→2.33 Å / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 7.1 / Num. unique obs: 698 / CC1/2: 0.987 / Rpim(I) all: 0.1 / Rrim(I) all: 0.207 / Χ2: 1.11

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.26→32.78 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 12.567 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.247 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25932 837 10.9 %RANDOM
Rwork0.20843 ---
obs0.21406 6828 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.888 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 2.26→32.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1066 0 35 25 1126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131116
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181049
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.6531510
X-RAY DIFFRACTIONr_angle_other_deg1.3611.6562428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5455137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85723.40447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.46215188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.373154
X-RAY DIFFRACTIONr_chiral_restr0.0880.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021218
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02220
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_it2.2462.903554
X-RAY DIFFRACTIONr_mcbond_other2.2482.896553
X-RAY DIFFRACTIONr_mcangle_it3.7284.322689
X-RAY DIFFRACTIONr_mcangle_other3.7254.33690
X-RAY DIFFRACTIONr_scbond_it3.0763.338562
X-RAY DIFFRACTIONr_scbond_other3.0733.338563
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8394.841822
X-RAY DIFFRACTIONr_long_range_B_refined7.53632.9961240
X-RAY DIFFRACTIONr_long_range_B_other7.53432.9921241
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.26→2.316 Å
RfactorNum. reflection% reflection
Rfree0.335 56 -
Rwork0.3 494 -
obs--98.04 %
Refinement TLS params.Method: refined / Origin x: 17.43 Å / Origin y: 5.152 Å / Origin z: -3.9721 Å
111213212223313233
T0.1619 Å2-0.0273 Å2-0.0022 Å2-0.1507 Å2-0.0198 Å2--0.0071 Å2
L0.3435 °2-0.2473 °2-0.3103 °2-0.1814 °20.2894 °2--2.1012 °2
S-0.0068 Å °0.044 Å °-0.0034 Å °0.0056 Å °-0.0309 Å °0.0061 Å °0.2052 Å °0.166 Å °0.0377 Å °

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