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- PDB-3wsj: HTLV-1 protease in complex with the HIV-1 protease inhibitor Indinavir -

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Basic information

Entry
Database: PDB / ID: 3wsj
TitleHTLV-1 protease in complex with the HIV-1 protease inhibitor Indinavir
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / retroviral protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
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-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY / Protease
Similarity search - Component
Biological speciesHuman T-lymphotropic virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.404 Å
AuthorsKuhnert, M. / Steuber, H. / Diederich, W.E.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structural basis for HTLV-1 protease inhibition by the HIV-1 protease inhibitor indinavir.
Authors: Kuhnert, M. / Steuber, H. / Diederich, W.E.
History
DepositionMar 14, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)27,19017
Polymers25,1332
Non-polymers2,05715
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-182 kcal/mol
Surface area11030 Å2
MethodPISA
2
A: Protease
B: Protease
hetero molecules

A: Protease
B: Protease
hetero molecules

A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,57051
Polymers75,3996
Non-polymers6,17145
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area27800 Å2
ΔGint-635 kcal/mol
Surface area29560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.260, 77.260, 159.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Protease /


Mass: 12566.579 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-116 / Mutation: L40I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-lymphotropic virus 1 / Gene: prt / Production host: Escherichia coli (E. coli) / References: UniProt: Q82134
#2: Chemical ChemComp-MK1 / N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE / INDINAVIR / Indinavir


Mass: 613.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H47N5O4
Comment: antivirus, antiretroviral, protease inhibitor, medication*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M imidazole, 0.2M lithium sulphate, 10% PEG 3000 , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 8, 2012
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.4→42 Å / Num. all: 11561 / Num. obs: 11561 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1813 / Rsym value: 0.648 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LIX

3lix


Resolution: 2.404→41.6 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 24.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 807 6.99 %RANDOM
Rwork0.2054 ---
all0.2088 11547 --
obs0.2088 11547 99.46 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.404→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 123 68 1956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031930
X-RAY DIFFRACTIONf_angle_d0.7042653
X-RAY DIFFRACTIONf_dihedral_angle_d13.371714
X-RAY DIFFRACTIONf_chiral_restr0.049324
X-RAY DIFFRACTIONf_plane_restr0.004322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.404-2.55460.30151290.26151734100
2.5546-2.75180.26441320.22031750100
2.7518-3.02860.24221320.21461758100
3.0286-3.46670.23921340.20111778100
3.4667-4.36690.25291350.1674179599
4.3669-41.6060.25831450.2179192598
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.92070.881-0.85452.922-0.58080.4950.3006-0.55890.23480.3016-0.2404-0.5882-0.11920.1933-0.05750.214-0.0483-0.03170.2480.05450.326151.8282-0.470321.4576
26.48090.264-0.74044.8239-0.55472.59550.106-0.00810.44680.3216-0.02130.33170.0573-0.2297-0.08550.19030.0105-0.02040.1354-0.00850.237525.34040.813120.7093
38.1872-0.49020.39033.98520.97996.7479-0.6155-0.9323-0.2460.55950.0161-0.75770.75470.8650.4160.59570.0943-0.09110.36250.110.411239.34550.59124.8276
41.64510.7357-1.7613.9916-1.68432.10470.9873-1.70220.71192.0048-0.5435-0.01170.3660.0122-0.44122.5317-0.5934-0.59681.6226-0.08141.520639.70197.397333.485
50.0674-0.0757-0.40510.23750.62292.6260.3089-1.77030.49611.5940.3160.1345-1.05630.5477-0.60091.9931-0.49410.58661.5396-0.20191.294536.9553-4.545734.8119
66.05362.12761.13142.66010.86060.42520.2133-0.25420.34640.207-0.2568-0.19660.0775-0.24280.07610.2877-0.02710.01510.23570.12430.321549.94783.788318.2728
75.72070.628-0.53092.9329-0.86341.3235-0.07460.06970.19540.2144-0.0130.2265-0.1676-0.07970.07520.15340.0149-0.04690.14650.01640.185927.3594-4.119218.7862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 1:54
2X-RAY DIFFRACTION2CHAIN B AND RESID 1:54
3X-RAY DIFFRACTION3CHAIN A AND RESID 201
4X-RAY DIFFRACTION4CHAIN A AND RESID 55:64
5X-RAY DIFFRACTION5CHAIN B AND RESID 55:64
6X-RAY DIFFRACTION6CHAIN A AND RESID 65:116
7X-RAY DIFFRACTION7CHAIN B AND RESID 65:116

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