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- PDB-6we7: HIV Integrase core domain in complex with inhibitor 3-methyl-2-{5... -

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Basic information

Entry
Database: PDB / ID: 6we7
TitleHIV Integrase core domain in complex with inhibitor 3-methyl-2-{5-methyl-2-[2-(thiophen-2-yl)ethynyl]-1- benzofuran-3-yl}butanoic 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 / host cell cytoplasm / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / proteolysis / DNA binding / zinc ion binding / membrane
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-TXM / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.28 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
DepositionApr 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1219
Polymers18,0481
Non-polymers1,0738
Water61334
1
A: Integrase
hetero molecules

A: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,24218
Polymers36,0972
Non-polymers2,14516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5370 Å2
ΔGint-156 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.111, 46.111, 140.220
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: 18048.494 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-TXM / (2S)-3-methyl-2-{5-methyl-2-[(thiophen-2-yl)ethynyl]-1-benzofuran-3-yl}butanoic acid


Mass: 338.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.07 Å3/Da / Density % sol: 40.48 % / 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: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 16, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.28→46.74 Å / Num. obs: 7524 / % possible obs: 99.7 % / Redundancy: 16.5 % / Biso Wilson estimate: 31.57 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.02 / Rrim(I) all: 0.082 / Χ2: 1.01 / Net I/σ(I): 34
Reflection shellResolution: 2.28→2.35 Å / Redundancy: 16.7 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 652 / CC1/2: 0.948 / Rpim(I) all: 0.174 / Rrim(I) all: 0.724 / Χ2: 1.04 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.28→43.8 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.885 / SU B: 14.235 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.282 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2936 715 9.6 %RANDOM
Rwork0.21784 ---
obs0.22511 6749 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.389 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.23 Å2
Refinement stepCycle: 1 / Resolution: 2.28→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1031 0 51 34 1116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131095
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171031
X-RAY DIFFRACTIONr_angle_refined_deg1.9321.671482
X-RAY DIFFRACTIONr_angle_other_deg1.3721.6032386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8965129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90623.26146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.61115185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.037154
X-RAY DIFFRACTIONr_chiral_restr0.0980.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021159
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02211
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_it2.3763.053528
X-RAY DIFFRACTIONr_mcbond_other2.3773.051527
X-RAY DIFFRACTIONr_mcangle_it3.8214.533653
X-RAY DIFFRACTIONr_mcangle_other3.8184.535654
X-RAY DIFFRACTIONr_scbond_it3.7783.594566
X-RAY DIFFRACTIONr_scbond_other3.7753.598567
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1435.261830
X-RAY DIFFRACTIONr_long_range_B_refined8.64236.8681232
X-RAY DIFFRACTIONr_long_range_B_other8.64336.8611232
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.338 Å
RfactorNum. reflection% reflection
Rfree0.438 43 -
Rwork0.237 482 -
obs--95.45 %
Refinement TLS params.Method: refined / Origin x: 16.8074 Å / Origin y: 4.4848 Å / Origin z: -4.0186 Å
111213212223313233
T0.0559 Å20.0102 Å2-0.0443 Å2-0.053 Å2-0.0426 Å2--0.0712 Å2
L0.6031 °2-0.605 °2-0.7734 °2-0.6127 °20.7507 °2--1.1311 °2
S-0.0027 Å °-0.0353 Å °-0.0641 Å °-0.019 Å °0.0191 Å °0.0828 Å °0.0474 Å °0.1219 Å °-0.0164 Å °

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