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

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Basic information

Entry
Database: PDB / ID: 6vlh
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-R2A / Integrase
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.036 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 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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)38,13218
Polymers35,7452
Non-polymers2,38816
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-128 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.306, 46.306, 139.148
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: 17872.305 Da / Num. of mol.: 2 / Fragment: core domain (UNP residues 50-211) / 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: F2WR39, RNA-directed DNA polymerase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: I
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-R2A / (2-{[3-(4-{2-[(3-{[3-(carboxymethyl)-5-methyl-1-benzofuran-2-yl]ethynyl}benzene-1-carbonyl)amino]ethyl}piperazine-1-carbonyl)phenyl]ethynyl}-5-methyl-1-benzofuran-3-yl)acetic acid


Mass: 761.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H39N3O8 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.8 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: MX2 / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 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: 2.036→46.38 Å / Num. obs: 18621 / % possible obs: 99.3 % / Redundancy: 8 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.021 / Rrim(I) all: 0.059 / Χ2: 1.06 / Net I/σ(I): 23.8
Reflection shellResolution: 2.036→2.09 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 1287 / Rpim(I) all: 0.172 / Rrim(I) all: 0.472 / Χ2: 1.2 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998-000)refinement
XDSdata reduction
PHENIXdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.036→46.306 Å / Cross valid method: THROUGHOUT / σ(F): 8.54 / Phase error: 37.22
RfactorNum. reflection% reflection
Rfree0.2981 3644 9.96 %
Rwork0.2095 --
obs0.2226 18621 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.036→46.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 108 54 2261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132239
X-RAY DIFFRACTIONf_angle_d1.5333030
X-RAY DIFFRACTIONf_dihedral_angle_d18.9111278
X-RAY DIFFRACTIONf_chiral_restr0.055334
X-RAY DIFFRACTIONf_plane_restr0.008367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0387-2.07380.30731670.31281561X-RAY DIFFRACTION86
2.0738-2.11150.38381800.31411735X-RAY DIFFRACTION91
2.1115-2.15210.40091760.30871604X-RAY DIFFRACTION90
2.1521-2.19610.36511960.32321709X-RAY DIFFRACTION90
2.1961-2.24380.6431720.4581519X-RAY DIFFRACTION87
2.2438-2.2960.61721710.47991628X-RAY DIFFRACTION86
2.296-2.35340.47431860.29851654X-RAY DIFFRACTION90
2.3534-2.4170.32971940.28621666X-RAY DIFFRACTION90
2.417-2.48810.30821700.27231639X-RAY DIFFRACTION91
2.4881-2.56840.35531860.26961693X-RAY DIFFRACTION90
2.5684-2.66020.3251860.271639X-RAY DIFFRACTION90
2.6602-2.76670.29521790.26011655X-RAY DIFFRACTION90
2.7667-2.89260.3081860.22571702X-RAY DIFFRACTION90
2.8926-3.0450.22511820.20211639X-RAY DIFFRACTION90
3.045-3.23570.35851880.19871649X-RAY DIFFRACTION90
3.2357-3.48540.21721810.1831661X-RAY DIFFRACTION90
3.4854-3.83590.27641910.1471662X-RAY DIFFRACTION89
3.8359-4.39020.19821770.12981635X-RAY DIFFRACTION90
4.3902-5.52860.22871910.12881648X-RAY DIFFRACTION90
5.5286-38.55540.2821710.19771624X-RAY DIFFRACTION88

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