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- PDB-5w5w: HIV Protease (PR) in open form with Mg2+ in active site and HIVE-... -

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Basic information

Entry
Database: PDB / ID: 5w5w
TitleHIV Protease (PR) in open form with Mg2+ in active site and HIVE-9 in eye site
ComponentsHIV-1 protease
KeywordsHYDROLASE / protease / allostery / fragment binding / exosite
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / 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
N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide / Chem-3TL / Chem-HV9 / Gag-Pol polyprotein / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsTiefenbrunn, T. / Stout, C.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1P50GM103368 United States
CitationJournal: to be published
Title: Fragment-based campaign for the identification of potential exosite binders of HIV-1 Protease
Authors: Forli, S. / Tiefenbrunn, T. / Baksh, M.M. / Chang, M.W. / Perryman, A. / Garg, D. / Happer, M. / Lin, Y.-C. / Goodsell, D. / Angelina, E.L. / De Vera, I. / Kojetin, D. / Torbett, B.E. / ...Authors: Forli, S. / Tiefenbrunn, T. / Baksh, M.M. / Chang, M.W. / Perryman, A. / Garg, D. / Happer, M. / Lin, Y.-C. / Goodsell, D. / Angelina, E.L. / De Vera, I. / Kojetin, D. / Torbett, B.E. / Finn, M.G. / Elder, J. / Stout, C.D. / Olson, A.
History
DepositionJun 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Structure summary / Category: pdbx_molecule_features
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9665
Polymers21,5352
Non-polymers1,4313
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: well known
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-27 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.846, 65.542, 92.876
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HIV-1 protease


Mass: 10767.702 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: PET 21A+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Q8V9, UniProt: P03366*PLUS
#2: Chemical ChemComp-3TL / benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate / TL-3, C2 symmetric inhibitor


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 909.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H64N6O10
References: N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide
#3: Chemical ChemComp-HV9 / 4-methyl-N-({1-[4-(trifluoromethyl)pyrimidin-2-yl]piperidin-4-yl}carbamoyl)benzene-1-sulfonamide


Mass: 443.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20F3N5O3S
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.04 Å3/Da / Density % sol: 39.66 % / Description: Rod
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 5000MME, 0.2M NH4I

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jan 15, 2015
RadiationMonochromator: multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→27.99 Å / Num. obs: 3674 / % possible obs: 97.8 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 4.64

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation27.99 Å3.11 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOLREP11.1.00phasing
PDB_EXTRACT3.22data extraction
PROTEUM PLUSdata collection
SHELXPREPdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EJK

4ejk


Resolution: 3→27.99 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.775 / SU B: 34.729 / SU ML: 0.635 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.657
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.325 173 4.5 %RANDOM
Rwork0.2438 ---
obs0.2475 3674 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 69 Å2 / Biso mean: 12.232 Å2 / Biso min: 2.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å20 Å2
2--0.07 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 3→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 100 1 1617
Biso mean--28.31 2.84 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021646
X-RAY DIFFRACTIONr_bond_other_d0.0020.021656
X-RAY DIFFRACTIONr_angle_refined_deg1.7452.0382232
X-RAY DIFFRACTIONr_angle_other_deg0.982.9953827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5945196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.51824.81554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14715284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.97158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211684
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02282
LS refinement shellResolution: 3→3.074 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.487 11 -
Rwork0.31 243 -
all-254 -
obs--94.78 %

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