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- PDB-6wc8: HIV Integrase core domain in complex with inhibitor 2-(5-(3-fluor... -

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Basic information

Entry
Database: PDB / ID: 6wc8
TitleHIV Integrase core domain in complex with inhibitor 2-(5-(3-fluorophenyl)-2-(2-(thiophen-2-yl)ethynyl)-1- benzofuran-3-yl)ethanoic acid
ComponentsIntegrase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / HIV Integrase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell / viral nucleocapsid / endonuclease activity / DNA recombination ...DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / RNA-directed DNA polymerase activity / host cell / viral nucleocapsid / endonuclease activity / DNA recombination / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Ribonuclease H-like superfamily/Ribonuclease H / 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 ...Ribonuclease H-like superfamily/Ribonuclease H / 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. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Chem-TQM / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.88 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 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,27010
Polymers18,0011
Non-polymers1,2689
Water46826
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,54020
Polymers36,0032
Non-polymers2,53718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5770 Å2
ΔGint-113 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.231, 46.231, 139.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

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Components

#1: Protein Integrase


Mass: 18001.486 Da / Num. of mol.: 1 / Fragment: 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: F2WR52, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-TQM / {5-(3-fluorophenyl)-2-[(thiophen-2-yl)ethynyl]-1-benzofuran-3-yl}acetic acid


Mass: 376.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H13FO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / 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: 2.07 Å3/Da / Density % sol: 40.52 % / Description: Bi-pyramid
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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9527 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 15, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9527 Å / Relative weight: 1
ReflectionResolution: 1.88→46.44 Å / Num. obs: 12966 / % possible obs: 98.4 % / Redundancy: 16.4 % / Biso Wilson estimate: 28.07 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.014 / Rrim(I) all: 0.057 / Χ2: 1.02 / Net I/σ(I): 39.4
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 15 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 6.6 / Num. unique obs: 617 / CC1/2: 0.969 / Rpim(I) all: 0.121 / Rrim(I) all: 0.499 / Χ2: 1.15 / % possible all: 75

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.88→43.88 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.003 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27817 1261 9.9 %RANDOM
Rwork0.23783 ---
obs0.24165 11469 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.843 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.82 Å20 Å2
3---1.64 Å2
Refinement stepCycle: 1 / Resolution: 1.88→43.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 51 26 1142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131137
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171056
X-RAY DIFFRACTIONr_angle_refined_deg2.1211.6661541
X-RAY DIFFRACTIONr_angle_other_deg1.421.5942445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3615137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.98123.67349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.32815193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.181154
X-RAY DIFFRACTIONr_chiral_restr0.0980.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021234
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02224
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_it2.1842.495554
X-RAY DIFFRACTIONr_mcbond_other2.1762.492553
X-RAY DIFFRACTIONr_mcangle_it3.6033.709689
X-RAY DIFFRACTIONr_mcangle_other3.6053.713690
X-RAY DIFFRACTIONr_scbond_it2.9522.949582
X-RAY DIFFRACTIONr_scbond_other2.4432.875567
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9124.168829
X-RAY DIFFRACTIONr_long_range_B_refined8.93630.2481284
X-RAY DIFFRACTIONr_long_range_B_other8.93830.2211281
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.925 Å
RfactorNum. reflection% reflection
Rfree0.594 58 -
Rwork0.497 638 -
obs--72.58 %
Refinement TLS params.Method: refined / Origin x: 17.9435 Å / Origin y: 6.2775 Å / Origin z: 4.2756 Å
111213212223313233
T0.0969 Å2-0.0237 Å2-0.0267 Å2-0.1251 Å2-0.0398 Å2--0.0314 Å2
L0.8164 °2-0.3329 °20.7648 °2-0.2235 °2-0.6057 °2--1.7999 °2
S0.0292 Å °-0.1221 Å °0.0989 Å °-0.0891 Å °0.0205 Å °-0.0004 Å °0.2378 Å °0.0888 Å °-0.0498 Å °

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