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- PDB-4ejd: HIV Protease (PR) dimer in closed form with pepstatin in active s... -

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Basic information

Entry
Database: PDB / ID: 4ejd
TitleHIV Protease (PR) dimer in closed form with pepstatin in active site and fragment 1F1 in the outside/top of flap
Components
  • Protease
  • pepstatin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / apo protease / allostery / fragment binding / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
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 ...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. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Pepstatin / 1H-indole-6-carboxylic acid / BETA-MERCAPTOETHANOL / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Streptomyces argenteolus subsp. toyonakensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.103 Å
AuthorsTiefenbrunn, T. / Stout, C.D.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Small molecule regulation of protein conformation by binding in the Flap of HIV protease.
Authors: Tiefenbrunn, T. / Forli, S. / Baksh, M.M. / Chang, M.W. / Happer, M. / Lin, Y.C. / Perryman, A.L. / Rhee, J.K. / Torbett, B.E. / Olson, A.J. / Elder, J.H. / Finn, M.G. / Stout, C.D.
History
DepositionApr 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
C: pepstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8378
Polymers22,3503
Non-polymers4885
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-40 kcal/mol
Surface area9510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.820, 65.630, 92.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein Protease / / PR / Retropepsin


Mass: 10831.833 Da / Num. of mol.: 2 / Fragment: UNP residues 490-588
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: R8 / Gene: pol / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: P12499, HIV-1 retropepsin
#2: Protein/peptide pepstatin / /


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 685.891 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Streptomyces argenteolus subsp. toyonakensis (bacteria)
References: Pepstatin

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Non-polymers , 4 types, 170 molecules

#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-1F1 / 1H-indole-6-carboxylic acid


Mass: 161.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 1.97 Å3/Da / Density % sol: 37.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.2 M potassium bromide, 0.2 M potassium thiocyanate, 3% PGA-LM, 3% MPD, 10% DMSO, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2010 / Details: Rh coated flat mirror
RadiationMonochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.103→92.93 Å / Num. all: 70609 / Num. obs: 70609 / % possible obs: 98.3 % / Redundancy: 3.4 % / Rsym value: 0.089 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.103-1.163.30.4831.534370103420.48399.9
1.16-1.233.40.3352.23316698020.33599.9
1.23-1.323.40.2622.83166192770.26299.9
1.32-1.423.40.1943.82948085870.19499.8
1.42-1.563.40.1275.62733179450.12799.9
1.56-1.743.40.0798.92466772350.07999.8
1.74-2.013.40.0688.12165263780.06899.6
2.01-2.473.20.0777.81712354280.07799.1
2.47-3.493.50.04314.21436141550.04396.6
3.49-21.9012.80.05210.8409314600.05257.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.98 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.8 Å21.9 Å
Translation1.8 Å21.9 Å

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Processing

Software
NameVersionClassificationNB
MOSFLM3.3.16data reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.103→18.96 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.1778 / WRfactor Rwork: 0.1467 / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.9194 / SU B: 0.934 / SU ML: 0.021 / SU R Cruickshank DPI: 0.0319 / SU Rfree: 0.0333 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 3543 5 %RANDOM
Rwork0.1459 ---
obs0.1475 70371 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.58 Å2 / Biso mean: 14.7297 Å2 / Biso min: 4.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.103→18.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 30 165 1757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191728
X-RAY DIFFRACTIONr_bond_other_d00.021194
X-RAY DIFFRACTIONr_angle_refined_deg1.4422.0172332
X-RAY DIFFRACTIONr_angle_other_deg2.06432972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8655215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.95624.51662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20215329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9031511
X-RAY DIFFRACTIONr_chiral_restr0.1390.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211834
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02304
X-RAY DIFFRACTIONr_rigid_bond_restr10.3332915
X-RAY DIFFRACTIONr_sphericity_free35.424566
X-RAY DIFFRACTIONr_sphericity_bonded10.97852987
LS refinement shellResolution: 1.103→1.132 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 216 -
Rwork0.262 4652 -
all-4868 -
obs--99.49 %

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