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- PDB-2qmp: Crystal Structure of HIV-1 protease complexed with PL-100 -

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Basic information

Entry
Database: PDB / ID: 2qmp
TitleCrystal Structure of HIV-1 protease complexed with PL-100
ComponentsPol polyprotein
KeywordsHYDROLASE / HIV-1 protease / Aspartyl protease / Multifunctional enzyme / Nucleotidyltransferase / RNA-directed DNA polymerase / Transferase
Function / homology
Function and homology information


viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / proteolysis / DNA binding
Similarity search - Function
Retropepsin-like catalytic domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Cathepsin D, subunit A; domain 1 / Acid Proteases ...Retropepsin-like catalytic domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-A00 / Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsAllison, T.J.
CitationJournal: To be Published
Title: Crystal Structure of HIV-1 protease complexed with PL-100
Authors: Coburn, C.A. / Allison, T.J. / Holloway, M.K. / Wu, J.J. / Wainberg, M.A. / Vacca, J.P.
History
DepositionJul 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9114
Polymers21,6622
Non-polymers1,2502
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.790, 85.980, 46.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Pol polyprotein


Mass: 10830.781 Da / Num. of mol.: 2 / Fragment: protease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WFL7, HIV-1 retropepsin
#2: Chemical ChemComp-A00 / N-[(5S)-5-{[(4-aminophenyl)sulfonyl](isobutyl)amino}-6-hydroxyhexyl]-Nalpha-(methoxycarbonyl)-beta-phenyl-L-phenylalaninamide


Mass: 624.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H44N4O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1:1 protein:reservoir, 6 mg/mL protein, 0.6 mM PL-100, protein buffer: 10 mM MES, 1 mM DTT, 1 mM EDTA, 3 mM NaN3, reservoir: 0.6 M NaCl, 100 mM NaOAc, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 11, 2006 / Details: Osmic VariMax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→47.96 Å / Num. obs: 21909 / % possible obs: 99.6 % / Redundancy: 4.38 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obs% possible all
1.8-1.864.30.3233.5100
1.86-1.944.310.2554.3100
1.94-2.034.350.1885.699.9
2.03-2.134.380.1676.299.7
2.13-2.274.410.1357.899.1
2.27-2.444.460.1148.699.2
2.44-2.694.460.0910.799.5
2.69-3.084.460.06713.999.8
3.08-3.884.430.04819.499.7
3.88-47.964.280.04224.599.3

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
d*TREKdata reduction
MOLREPphasing
RefinementResolution: 1.8→47.96 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / SU B: 2.955 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24783 1125 5.1 %RANDOM
Rwork0.20502 ---
obs0.20729 20770 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.741 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2---0.54 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 88 244 1850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221636
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1832.0422216
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4365196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.942556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97215284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.721158
X-RAY DIFFRACTIONr_chiral_restr0.0680.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021172
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.2754
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21127
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2184
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5921.51028
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89721602
X-RAY DIFFRACTIONr_scbond_it1.4623701
X-RAY DIFFRACTIONr_scangle_it2.3274.5614
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 90 -
Rwork0.314 1506 -
obs--100 %

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