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- PDB-3vq9: HIV-1 IN core domain in complex with 6-fluoro-1,3-benzothiazol-2-amine -

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Basic information

Entry
Database: PDB / ID: 3vq9
TitleHIV-1 IN core domain in complex with 6-fluoro-1,3-benzothiazol-2-amine
ComponentsPOL polyprotein
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / RNaseH / DNA binding / DNA cleavage / DNA integration / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / host cell / viral nucleocapsid / DNA recombination / aspartic-type endopeptidase activity / 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 / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral ...Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / 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. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
6-fluoro-1,3-benzothiazol-2-amine / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWielens, J. / Chalmers, D.K. / Parker, M.W. / Scanlon, M.J.
CitationJournal: J Biomol Screen / Year: 2013
Title: Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification?
Authors: Wielens, J. / Headey, S.J. / Rhodes, D.I. / Mulder, R.J. / Dolezal, O. / Deadman, J.J. / Newman, J. / Chalmers, D.K. / Parker, M.W. / Peat, T.S. / Scanlon, M.J.
History
DepositionMar 20, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POL polyprotein
B: POL polyprotein
C: POL polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1584
Polymers52,9893
Non-polymers1681
Water2,990166
1
A: POL polyprotein
B: POL polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4943
Polymers35,3262
Non-polymers1681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-21 kcal/mol
Surface area12620 Å2
MethodPISA
2
C: POL polyprotein

C: POL polyprotein


Theoretical massNumber of molelcules
Total (without water)35,3262
Polymers35,3262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2950 Å2
ΔGint-18 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.327, 72.909, 79.851
Angle α, β, γ (deg.)90.00, 108.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein POL polyprotein


Mass: 17663.154 Da / Num. of mol.: 3 / Fragment: integrase core domain, UNP residues 765-925 / Mutation: F185H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL43 / Gene: pol / Plasmid: PeT23b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q72498
#2: Chemical ChemComp-FBB / 6-fluoro-1,3-benzothiazol-2-amine


Mass: 168.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5FN2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.4M SODIUM CITRATE, 50mM HEPES PH 7.5, 7.5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94937 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 2, 2007
RadiationMonochromator: double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94937 Å / Relative weight: 1
ReflectionResolution: 1.9→75.6 Å / Num. all: 42674 / Num. obs: 42469 / % possible obs: 99.52 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 17.5
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.299 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1bl3

1bl3


Resolution: 1.9→75.59 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23202 2143 5 %RANDOM
Rwork0.19578 ---
all0.1958 42469 --
obs0.1976 40326 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.056 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20 Å20.55 Å2
2---0.04 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 1.9→75.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3419 0 11 166 3596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223501
X-RAY DIFFRACTIONr_bond_other_d00.022304
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.9284740
X-RAY DIFFRACTIONr_angle_other_deg4.11835648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9495435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57924.726146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05215603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.371512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023855
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02677
X-RAY DIFFRACTIONr_nbd_refined0.2130.2748
X-RAY DIFFRACTIONr_nbd_other0.2550.22122
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21750
X-RAY DIFFRACTIONr_nbtor_other0.110.21459
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2149
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2431.52173
X-RAY DIFFRACTIONr_mcbond_other01.5907
X-RAY DIFFRACTIONr_mcangle_it2.14123498
X-RAY DIFFRACTIONr_scbond_it3.00431328
X-RAY DIFFRACTIONr_scangle_it4.5354.51242
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 171 -
Rwork0.248 2965 -
obs--100 %

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