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- PDB-3ou3: MDR769 HIV-1 protease complexed with PR/RT hepta-peptide -

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Basic information

Entry
Database: PDB / ID: 3ou3
TitleMDR769 HIV-1 protease complexed with PR/RT hepta-peptide
Components
  • HIV-1 protease
  • PR/RT substrate peptide
KeywordsHYDROLASE/PEPTIDE / MDR HIV-1 protease / inhibitor / drug resistance / substrate envelope / HIV-1 protease / protease / PR/RT substrate peptide / none / HYDROLASE / HYDROLASE-PEPTIDE complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / endonuclease activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Gag-Pol polyprotein / Pol protein / Pol protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLiu, Z. / Wang, Y. / Brunzelle, J. / Kovari, I.A. / Kovari, L.C.
CitationJournal: Protein J. / Year: 2011
Title: Nine Crystal Structures Determine the Substrate Envelope of the MDR HIV-1 Protease.
Authors: Liu, Z. / Wang, Y. / Brunzelle, J. / Kovari, I.A. / Kovari, L.C.
History
DepositionSep 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 protease
B: HIV-1 protease
C: PR/RT substrate peptide


Theoretical massNumber of molelcules
Total (without water)22,3263
Polymers22,3263
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-21 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.621, 45.621, 102.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsHIV-1 protease dimer binds with one PR/RT substrate peptide

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Components

#1: Protein HIV-1 protease


Mass: 10769.635 Da / Num. of mol.: 2
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: Q000H7, UniProt: P35963*PLUS
#2: Protein/peptide PR/RT substrate peptide


Mass: 786.915 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in HIV-1 / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YV20, UniProt: P35963*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.8M NaCl 01 M MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2008
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→46.67 Å / Num. all: 22908 / Num. obs: 22519 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)% possible all
1.7-1.7697.2
1.76-1.8397.6
1.83-1.9197.9
1.91-2.0298.1
2.02-2.1498.3
2.14-2.3198.6
2.31-2.5499
2.54-2.9199.1
2.91-3.6699.4
3.66-34.0298.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→41.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.123 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22634 1140 5.1 %RANDOM
Rwork0.19326 ---
all0.19326 21736 --
obs0.19495 21376 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.977 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1569 0 0 247 1816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221600
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9832178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.3642558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7615279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.529158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021167
X-RAY DIFFRACTIONr_nbd_refined0.2210.2711
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2151
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.220
X-RAY DIFFRACTIONr_mcbond_it1.3661.51053
X-RAY DIFFRACTIONr_mcangle_it1.64521662
X-RAY DIFFRACTIONr_scbond_it2.6653626
X-RAY DIFFRACTIONr_scangle_it4.3514.5516
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 85 -
Rwork0.258 1531 -
obs--97.23 %

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