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- PDB-6vka: HIV Integrase Core domain (IN) in complex with dimer-spanning ligand -

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Basic information

Entry
Database: PDB / ID: 6vka
TitleHIV Integrase Core domain (IN) in complex with dimer-spanning ligand
ComponentsIntegrase
KeywordsTRANSFERASE / Virus / Inhibitor / Complex / HIV Integrase
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 / DNA binding / 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-QZV / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.863 Å
AuthorsGorman, M.A. / Parker, M.W.
CitationJournal: To Be Published
Title: HIV Integrase core domain (IN) in complex with dimeric spanning inhibitor
Authors: Scanlon, M. / Gorman, M.A.
History
DepositionJan 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 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: Integrase
B: Integrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,50619
Polymers36,0032
Non-polymers2,50317
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-166 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.302, 46.302, 138.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Integrase


Mass: 18001.420 Da / Num. of mol.: 2 / Fragment: UNP residues 50-212 / Mutation: Q53E, C56S, W131E, 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, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-QZV / 2,2'-{ethane-1,2-diylbis[oxyethane-2,1-diylcarbamoyl-4,1-phenyleneethyne-2,1-diyl(5-methyl-1-benzofuran-2,3-diyl)]}diacetic acid


Mass: 780.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H40N2O10 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 40.15 % / Description: Bi-pyramid
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 2.2 M ammonium sulfate, 200 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: 0.96 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 10, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.86→46.34 Å / Num. obs: 23848 / % possible obs: 98.59 % / Redundancy: 8.6 % / Biso Wilson estimate: 22.92 Å2 / CC1/2: 0.99 / CC star: 1 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.03 / Rrim(I) all: 0.088 / Net I/av σ(I): 23.57 / Net I/σ(I): 23.57
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 3.03 / Num. unique obs: 2344 / CC1/2: 0.735 / CC star: 0.92 / Rpim(I) all: 0.277 / Rrim(I) all: 0.816 / % possible all: 96.58

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.863→46.302 Å / Cross valid method: THROUGHOUT / σ(F): 19.31 / Phase error: 30.21
RfactorNum. reflection% reflection
Rfree0.2122 4020 8.53 %
Rwork0.1448 --
obs0.163 23848 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.863→46.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 114 92 2396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122344
X-RAY DIFFRACTIONf_angle_d1.5113175
X-RAY DIFFRACTIONf_dihedral_angle_d17.2721342
X-RAY DIFFRACTIONf_chiral_restr0.061352
X-RAY DIFFRACTIONf_plane_restr0.009387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8646-1.89680.30221940.24352125X-RAY DIFFRACTION89
1.8968-1.93130.27441980.24072173X-RAY DIFFRACTION89
1.9313-1.96840.26582000.22792058X-RAY DIFFRACTION89
1.9684-2.00860.30962080.20432171X-RAY DIFFRACTION89
2.0086-2.05220.29121960.21412144X-RAY DIFFRACTION90
2.0522-2.10.24571980.19562128X-RAY DIFFRACTION90
2.1-2.15240.25221950.18352141X-RAY DIFFRACTION90
2.1524-2.21060.20441870.18262196X-RAY DIFFRACTION91
2.2106-2.27560.22411840.1662129X-RAY DIFFRACTION91
2.2756-2.34910.21552060.16612163X-RAY DIFFRACTION90
2.3491-2.4330.2742080.15632170X-RAY DIFFRACTION90
2.433-2.53030.21481960.1542126X-RAY DIFFRACTION90
2.5303-2.64540.24532040.14662152X-RAY DIFFRACTION90
2.6454-2.78470.21892060.14992140X-RAY DIFFRACTION90
2.7847-2.9590.19342120.13672198X-RAY DIFFRACTION90
2.959-3.18720.20571940.13532154X-RAY DIFFRACTION91
3.1872-3.50740.19681960.14572185X-RAY DIFFRACTION91
3.5074-4.01360.19742040.13372181X-RAY DIFFRACTION91
4.0136-5.05160.18682200.12892186X-RAY DIFFRACTION91
5.0516-27.67440.2452060.16632156X-RAY DIFFRACTION91

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