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- PDB-9zvr: Crystal structure of HTLV-1 protease bound to darunavir at 2.1 an... -

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Basic information

Entry
Database: PDB / ID: 9zvr
TitleCrystal structure of HTLV-1 protease bound to darunavir at 2.1 angstroms with truncated flaps
ComponentsHTLV-1 Protease
KeywordsVIRAL PROTEIN/INHIBITOR / HTLV-1 / PROTEASE / DRUG RESISTANCE / PROTEASE INHIBITOR / COMPLEX / HYDROLASE INHIBITOR COMPLEX / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / VIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Chem-017 / PHOSPHATE ION / Pro protein
Similarity search - Component
Biological speciesHuman T-cell leukemia virus type I
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShaqra, A.M. / Lockbaum, G.J. / Intravaia, L.E. / Schiffer, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01-GM109767 United States
CitationJournal: To Be Published
Title: Crystal structure of HTLV-1 protease bound to darunavir at 2.1 angstroms with truncated flaps
Authors: Shaqra, A.M. / Lockbaum, G.J. / Intravaia, L.E. / Schiffer, C.A.
History
DepositionDec 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: HTLV-1 Protease
A: HTLV-1 Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2388
Polymers25,1332
Non-polymers1,1056
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.477, 77.477, 160.444
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-202-

PO4

21A-342-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 9 or resid 11...
d_2ens_1(chain "B" and (resid 1 through 9 or resid 11...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROARGARGAB1 - 91 - 9
d_12PROPROVALVALAB11 - 1211 - 12
d_13ALAALAASPASPAB15 - 1815 - 18
d_14GLNGLNGLNGLNAB2020
d_15HISHISVALVALAB23 - 3923 - 39
d_16PROPROSERSERAB41 - 4641 - 46
d_17ASNASNTHRTHRAB48 - 5448 - 54
d_18ASPASPTHRTHRAB65 - 7065 - 70
d_19LEULEUTHRTHRAB72 - 8872 - 88
d_110LEULEUILEILEAB91 - 10091 - 100
d_111GLYGLYGLNGLNAB102 - 108102 - 108
d_112GLNGLNPROPROAB110 - 116110 - 116
d_21PROPROARGARGBA1 - 91 - 9
d_22PROPROVALVALBA11 - 1211 - 12
d_23ALAALAASPASPBA15 - 1815 - 18
d_24GLNGLNGLNGLNBA2020
d_25HISHISVALVALBA23 - 3923 - 39
d_26PROPROTHRTHRBA41 - 7041 - 70
d_27LEULEUTHRTHRBA72 - 8872 - 88
d_28LEULEUILEILEBA91 - 10091 - 100
d_29GLYGLYGLNGLNBA102 - 108102 - 108
d_210GLNGLNPROPROBA110 - 116110 - 116

NCS oper: (Code: givenMatrix: (-0.976145347149, 0.0283377355677, -0.215260851021), (-0.0130722110452, -0.997318100221, -0.0720119730957), (-0.216724199243, -0.0674802172021, 0.973897860019)Vector: - ...NCS oper: (Code: given
Matrix: (-0.976145347149, 0.0283377355677, -0.215260851021), (-0.0130722110452, -0.997318100221, -0.0720119730957), (-0.216724199243, -0.0674802172021, 0.973897860019)
Vector: -43.5275142971, 65.2032099525, -2.49352661903)

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein HTLV-1 Protease


Mass: 12566.579 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-cell leukemia virus type I / Gene: pro / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y1C9N2

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Non-polymers , 5 types, 100 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-017 / (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE / Darunavir / TMC114 / UIC-94017


Mass: 547.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H37N3O7S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antiretroviral*YM
#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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 39-41% (v/v) PEG 300, 0.1M Phosphate/Citrate Buffer pH 4.2

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.07812 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 2.1→41.82 Å / Num. obs: 34752 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 49.07 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.013 / Rpim(I) all: 0.013 / Rrim(I) all: 0.018 / Net I/σ(I): 19
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3354 / CC1/2: 0.749 / Rpim(I) all: 0.278 / Rrim(I) all: 0.394

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→41.82 Å / SU ML: 0.253 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7099
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2529 869 5 %
Rwork0.216 16502 -
obs0.2179 17371 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 0 70 94 1744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121813
X-RAY DIFFRACTIONf_angle_d1.49752511
X-RAY DIFFRACTIONf_chiral_restr0.0771318
X-RAY DIFFRACTIONf_plane_restr0.0085309
X-RAY DIFFRACTIONf_dihedral_angle_d8.3558267
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.13311813989 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.230.29671400.26022659X-RAY DIFFRACTION100
2.23-2.40.34061420.27312690X-RAY DIFFRACTION100
2.4-2.650.29171410.262691X-RAY DIFFRACTION100
2.65-3.030.30761440.26112726X-RAY DIFFRACTION99.93
3.03-3.810.26471450.21962770X-RAY DIFFRACTION99.93
3.82-41.820.21561570.18712966X-RAY DIFFRACTION99.94

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