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- PDB-3vq4: Fragments bound to HIV-1 integrase -

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Basic information

Entry
Database: PDB / ID: 3vq4
TitleFragments bound to HIV-1 integrase
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 / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell ...exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
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
(5-phenyl-1,2-oxazol-3-yl)methanol / : / 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,56810
Polymers34,4972
Non-polymers1,0718
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-60 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.601, 62.323, 82.087
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein POL polyprotein


Mass: 17248.518 Da / Num. of mol.: 2
Fragment: Integrase CATALYTIC CORE DOMAIN, UNP residues 770-927
Mutation: C56S W131D, F139D, 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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-0NX / (5-phenyl-1,2-oxazol-3-yl)methanol


Mass: 175.184 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H9NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.6M AmSO4, 0.1M Na Citrate pH 5.6, 50mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 7, 2007
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.9→49.63 Å / Num. all: 25133 / Num. obs: 25118 / % possible obs: 99.98 % / Rmerge(I) obs: 0.108 / Rsym value: 0.117 / Net I/σ(I): 13.5
Reflection shellResolution: 1.9→2 Å / % possible all: 99.98

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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 3l3u

3l3u


Resolution: 1.9→49.63 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.904 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25118 1267 5 %RANDOM
Rwork0.20846 ---
all0.2085 25113 --
obs0.21068 23866 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.541 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2--0.74 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 48 83 2306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222261
X-RAY DIFFRACTIONr_bond_other_d0.0010.021488
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.9563056
X-RAY DIFFRACTIONr_angle_other_deg1.12433646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6015280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.6582592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.80715387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.777158
X-RAY DIFFRACTIONr_chiral_restr0.2550.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022491
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02431
X-RAY DIFFRACTIONr_nbd_refined0.2140.2470
X-RAY DIFFRACTIONr_nbd_other0.2020.21432
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21040
X-RAY DIFFRACTIONr_nbtor_other0.090.21101
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.2105
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.4090.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.9770.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7371.51819
X-RAY DIFFRACTIONr_mcbond_other0.3511.5586
X-RAY DIFFRACTIONr_mcangle_it2.06622245
X-RAY DIFFRACTIONr_scbond_it331001
X-RAY DIFFRACTIONr_scangle_it3.9974.5811
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
Rfree0.369 79 -
Rwork0.311 1732 -
obs--99.94 %

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