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- PDB-3liq: Crystal Structure of HTLV protease complexed with the inhibitor, ... -

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Basic information

Entry
Database: PDB / ID: 3liq
TitleCrystal Structure of HTLV protease complexed with the inhibitor, KNI-10673
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-10673 / Chem-E14 / Protease
Similarity search - Component
Biological speciesHuman T-lymphotropic virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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 / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7733
Polymers25,1332
Non-polymers6401
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-24 kcal/mol
Surface area10900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.950, 77.950, 163.204
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 / 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-E14 / (4R)-3-[(2S,3S)-3-[[(2S)-2-[[(2S)-2-azanyl-2-phenyl-ethanoyl]amino]-3,3-dimethyl-butanoyl]amino]-2-hydroxy-4-phenyl-but anoyl]-5,5-dimethyl-N-(2-methylpropyl)-1,3-thiazolidine-4-carboxamide / KNI-10673


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 639.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H49N5O5S / References: KNI-10673
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 17% PEG8000, 16% PEG300, 10mM DTT and 0,2M KH2PO4, 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: Dec 30, 2008
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 13688 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rsym value: 0.093 / Net I/σ(I): 21.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.221 / % possible all: 92.3

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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: 2.29→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 12.335 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23433 428 3.1 %RANDOM
Rwork0.18844 ---
obs0.18989 13232 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.207 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å2-0.8 Å20 Å2
2---1.61 Å20 Å2
3---2.41 Å2
Refinement stepCycle: LAST / Resolution: 2.29→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 45 83 1894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221864
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6052.0192564
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7775236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.8724.51662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.46515304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0971510
X-RAY DIFFRACTIONr_chiral_restr0.1020.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0221359
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_it2.38921185
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.83831961
X-RAY DIFFRACTIONr_scbond_it2.9362679
X-RAY DIFFRACTIONr_scangle_it4.3873600
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.294→2.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 28 -
Rwork0.213 827 -
obs--86.36 %
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)
11.0805-0.2283-0.42044.2230.12230.6786-0.07190.10890.2080.2090.0089-0.2911-0.0238-0.02380.0629-0.0702-0.0128-0.0624-0.07440.0314-0.029723.356344.760820.9662
22.30750.25210.17973.4559-0.6330.6826-0.12630.1092-0.22060.05460.04720.10390.02450.02360.0791-0.0604-0.00370.0092-0.07-0.0289-0.073115.121722.808820.8531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 116
2X-RAY DIFFRACTION2B1 - 116

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