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- PDB-7l23: HIV Integrase core domain in complex with inhibitor 2-(5-(3-fluor... -

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Basic information

Entry
Database: PDB / ID: 7l23
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 / RNA stem-loop binding / RNA-directed DNA polymerase activity / endonuclease activity / DNA recombination / symbiont entry into host cell / zinc ion binding
Similarity search - Function
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 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. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
IODIDE ION / Chem-XFS / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsGorman, M.A. / Parker, M.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
Not funded Australia
CitationJournal: To Be Published
Title: Rapid development of potent inhibitors of the HIV integrase-LEDGF interaction by fragment-linking using off-rate screening
Authors: Chiew, B. / Scanlon, M.J.
History
DepositionDec 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)17,4859
Polymers16,3241
Non-polymers1,1618
Water30617
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,96918
Polymers32,6472
Non-polymers2,32216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5180 Å2
ΔGint-59 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.270, 46.270, 138.710
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: 16323.608 Da / Num. of mol.: 1 / Fragment: UNP residues 57-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q76353
#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.: 5 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-XFS / 3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzoic acid


Mass: 334.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H14O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 45.91 % / Description: Bi-pyramid
Crystal growTemperature: 294 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 18, 2015 / Details: AXCO Capillary optics
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→34.68 Å / Num. obs: 7697 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 36.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.02 / Rrim(I) all: 0.046 / Net I/σ(I): 18.1
Reflection shellResolution: 2.26→2.33 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.198 / Num. unique obs: 690 / CC1/2: 0.989 / Rpim(I) all: 0.1 / Rrim(I) all: 0.222 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
d*TREKdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VQA

3vqa


Resolution: 2.26→34.7 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.27 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27955 800 10.5 %RANDOM
Rwork0.21589 ---
obs0.22265 6815 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.786 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å2-0 Å2
2--1.1 Å2-0 Å2
3----2.19 Å2
Refinement stepCycle: 1 / Resolution: 2.26→34.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1049 0 40 17 1106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131108
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181059
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.6561501
X-RAY DIFFRACTIONr_angle_other_deg1.2621.5942437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3395137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76623.40447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.60715189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.042154
X-RAY DIFFRACTIONr_chiral_restr0.0650.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021233
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02240
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_it3.894.566548
X-RAY DIFFRACTIONr_mcbond_other3.874.559547
X-RAY DIFFRACTIONr_mcangle_it5.8836.81682
X-RAY DIFFRACTIONr_mcangle_other5.8796.817683
X-RAY DIFFRACTIONr_scbond_it4.6265.08559
X-RAY DIFFRACTIONr_scbond_other4.6225.077560
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2777.383819
X-RAY DIFFRACTIONr_long_range_B_refined10.61552.0871242
X-RAY DIFFRACTIONr_long_range_B_other10.61252.0811243
LS refinement shellResolution: 2.26→2.316 Å
RfactorNum. reflection% reflection
Rfree0.337 59 -
Rwork0.274 472 -
obs--95.68 %

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