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- PDB-5vck: HIV Protease (PR) with TL-3 in the active site and (Z)-N-(thiazol... -

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Basic information

Entry
Database: PDB / ID: 5vck
TitleHIV Protease (PR) with TL-3 in the active site and (Z)-N-(thiazol-2-yl)-N'-tosylcarbamimidate in the exosite
ComponentsProtease
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 / 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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / 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 / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal 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) / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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
N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide / Chem-3TL / Chem-7GC / Gag-Pol polyprotein / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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
DepositionMar 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 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: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1675
Polymers21,6642
Non-polymers1,5043
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: well established
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-28 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.953, 62.953, 82.306
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protease


Mass: 10831.833 Da / Num. of mol.: 2 / Mutation: Q7K
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): Bl21(DE3)
References: UniProt: Q90EA1, UniProt: P12497*PLUS, HIV-1 retropepsin
#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-7GC / 4-methyl-N-(thiazol-2-ylcarbamoyl)benzenesulfonamide / 4-methyl-N-[(1,3-thiazol-2-yl)carbamoyl]benzene-1-sulfonamide


Mass: 297.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11N3O3S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.18 Å3/Da / Density % sol: 43.71 % / Description: flat plates
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 1.3M NH4SO4, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: May 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.701→32.846 Å / Num. obs: 20325 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Rsym value: 0.053 / Net I/av σ(I): 7.989 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.701-1.794.81.6350.50.8281.841.63598.9
1.79-1.96.90.960.80.3921.0370.96100
1.9-2.036.60.5371.40.2260.5840.53799.9
2.03-2.26.80.25830.1070.2790.258100
2.2-2.416.70.1550.0630.1630.15100
2.41-2.696.70.0839.10.0340.090.083100
2.69-3.116.90.04715.30.0190.0510.047100
3.11-3.86.70.03218.20.0130.0350.032100
3.8-5.386.50.03117.90.0130.0330.031100
5.38-32.8466.50.02815.80.0120.0310.02899.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.85 Å
Translation2.5 Å32.85 Å

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
autoXDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EJK

4ejk


Resolution: 1.8→32.846 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.839 / SU ML: 0.084 / SU R Cruickshank DPI: 0.3578 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.358 / ESU R Free: 0.125
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 861 5 %RANDOM
Rwork0.1735 ---
obs0.1755 16309 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.82 Å2 / Biso mean: 39.775 Å2 / Biso min: 19.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 1.8→32.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 104 42 1658
Biso mean--45.41 54.35 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191657
X-RAY DIFFRACTIONr_bond_other_d0.0020.021619
X-RAY DIFFRACTIONr_angle_refined_deg1.8542.0562248
X-RAY DIFFRACTIONr_angle_other_deg0.99233717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.175198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.42124.6354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15315283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.778158
X-RAY DIFFRACTIONr_chiral_restr0.0930.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211802
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02334
X-RAY DIFFRACTIONr_mcbond_it2.4793.79792
X-RAY DIFFRACTIONr_mcbond_other2.483.789791
X-RAY DIFFRACTIONr_mcangle_it2.8895.676987
X-RAY DIFFRACTIONr_rigid_bond_restr1.20833276
X-RAY DIFFRACTIONr_sphericity_free27.711523
X-RAY DIFFRACTIONr_sphericity_bonded8.553262
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 61 -
Rwork0.117 1201 -
all-1262 -
obs--99.76 %

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