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- PDB-3lix: crystal structure of htlv protease complexed with the inhibitor K... -

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Basic information

Entry
Database: PDB / ID: 3lix
Titlecrystal structure of htlv protease complexed with the inhibitor KNI-10729
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / 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
KNI-10729 / Chem-E17 / Protease
Similarity search - Component
Biological speciesHuman T-lymphotropic virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSatoh, T. / Li, M. / Nguyen, J. / Kiso, Y. / Wlodawer, A. / Gustchina, A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structures of inhibitor complexes of human T-cell leukemia virus (HTLV-1) protease.
Authors: Satoh, T. / Li, M. / Nguyen, J.T. / Kiso, Y. / Gustchina, A. / Wlodawer, A.
History
DepositionJan 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)25,9944
Polymers25,1332
Non-polymers8602
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-24 kcal/mol
Surface area10750 Å2
MethodPISA
2
A: Protease
B: Protease
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)155,96224
Polymers150,79912
Non-polymers5,16312
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area33270 Å2
ΔGint-402 kcal/mol
Surface area58000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.376, 77.376, 159.327
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

#1: Protein Protease


Mass: 12566.579 Da / Num. of mol.: 2 / Mutation: L40I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-lymphotropic virus 1 / Gene: prt / Plasmid: pHTLVdelta9 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: Q82134
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-E17 / N-{(1S,2S)-1-benzyl-3-[(4R)-5,5-dimethyl-4-{[(1R)-1,2,2-trimethylpropyl]carbamoyl}-1,3-thiazolidin-3-yl]-2-hydroxy-3-oxopropyl}-3-methyl-N~2~-{(2S)-2-[(morpholin-4-ylacetyl)amino]-2-phenylacetyl}-L-valinamide / KNI-10729


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 795.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H62N6O7S / References: KNI-10729
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 17%PEG8000 16% PEG300 0.01M BaCl 10mM DTT, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 2008
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 7455 / % possible obs: 89.4 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rsym value: 0.101 / Net I/σ(I): 14.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.28 / % possible all: 59.4

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.4.0057refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B7F

2b7f


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.871 / SU B: 27.017 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28165 214 2.9 %RANDOM
Rwork0.20559 ---
obs0.20764 7237 89.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.229 Å2
Baniso -1Baniso -2Baniso -3
1--4.15 Å2-2.07 Å20 Å2
2---4.15 Å20 Å2
3---6.22 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 57 55 1878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221871
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5482.0252571
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9935234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96324.51662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.85415303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3871510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221360
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.01621182
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.36831954
X-RAY DIFFRACTIONr_scbond_it4.5032689
X-RAY DIFFRACTIONr_scangle_it6.8633615
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 875 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.550.5
medium thermal0.982
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 11 -
Rwork0.228 335 -
obs--58.54 %
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)
11.26040.2358-0.38173.52890.10380.3666-0.0453-0.01870.47340.0233-0.00220.0198-0.0466-0.04180.04750.04480.0232-0.06530.0373-0.00430.128723.487744.391120.5827
22.13110.56310.25932.9459-0.49651.6701-0.17330.0485-0.1665-0.0450.05170.37570.0023-0.0210.12160.04360.01080.00660.03330.0060.071615.215822.652920.7086
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 116
2X-RAY DIFFRACTION2B1 - 116

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