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- PDB-4tvh: HIV Protease (PR) dimer in closed form with TL-3 in active site a... -

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Basic information

Entry
Database: PDB / ID: 4tvh
TitleHIV Protease (PR) dimer in closed form with TL-3 in active site and fragment AK-2097 in the outside/top of flap
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV protease / allostery / fragment binding / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide / Chem-3TL / BETA-MERCAPTOETHANOL / Chem-K97 / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.195 Å
AuthorsTiefenbrunn, T. / Kislukhin, A. / Finn, M.G. / Stout, C.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103368-02 United States
CitationJournal: J.Phys.Chem.B / Year: 2015
Title: Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease.
Authors: Deng, N. / Forli, S. / He, P. / Perryman, A. / Wickstrom, L. / Vijayan, R.S. / Tiefenbrunn, T. / Stout, D. / Gallicchio, E. / Olson, A.J. / Levy, R.M.
History
DepositionJun 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9115
Polymers21,6642
Non-polymers1,2473
Water1,06359
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-35 kcal/mol
Surface area9670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.916, 66.295, 92.175
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Protease /


Mass: 10831.833 Da / Num. of mol.: 2 / Fragment: HIV protease
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: Q90EA1
#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 / Fragment: TL-3 / Source method: obtained synthetically / Formula: C50H64N6O10
References: N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-K97 / 3-(morpholin-4-ylmethyl)-1H-indole-6-carboxylic acid


Mass: 260.288 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2.4M NaFormate, 10% DMSO, pH4.6 NaOAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 A
DetectorType: APEX II CCD / Detector: CCD / Date: Jan 5, 2011
RadiationMonochromator: multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.195→53.82 Å / Num. obs: 9437 / % possible obs: 98.3 % / Redundancy: 3.6 % / Net I/σ(I): 10.02
Reflection shellResolution: 2.195→2.24 Å / Redundancy: 1.73 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.29

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.25 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.2 Å31.19 Å
Translation2.2 Å31.19 Å

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
PHASERphasing
PROTEUMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KFR

3kfr


Resolution: 2.195→31.19 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.1598 / FOM work R set: 0.8491 / SU B: 6.225 / SU ML: 0.161 / SU R Cruickshank DPI: 0.3502 / SU Rfree: 0.2509 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.35 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 451 4.8 %RANDOM
Rwork0.1837 8986 --
obs0.1871 9437 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.24 Å2 / Biso mean: 19.2 Å2 / Biso min: 8.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.04 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 2.195→31.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 89 59 1664
Biso mean--21.57 20.84 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191640
X-RAY DIFFRACTIONr_bond_other_d0.0010.021672
X-RAY DIFFRACTIONr_angle_refined_deg1.9482.0462218
X-RAY DIFFRACTIONr_angle_other_deg1.37733839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2645196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.28524.44454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93815288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.823159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02318
X-RAY DIFFRACTIONr_mcbond_it1.4881.778791
X-RAY DIFFRACTIONr_mcbond_other1.4891.778790
X-RAY DIFFRACTIONr_mcangle_it2.4122.662984
LS refinement shellResolution: 2.195→2.251 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 28 -
Rwork0.204 554 -
all-582 -
obs--84.35 %

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