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- PDB-2p7u: The crystal structure of rhodesain, the major cysteine protease o... -

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Basic information

Entry
Database: PDB / ID: 2p7u
TitleThe crystal structure of rhodesain, the major cysteine protease of T. brucei rhodesiense, bound to inhibitor K777
ComponentsCysteine protease
KeywordsHYDROLASE / cysteine protease / trypanosoma brucei / neglected disease
Function / homology
Function and homology information


proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function
Domain of unknown function DUF3586 / Protein of unknown function (DUF3586) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. ...Domain of unknown function DUF3586 / Protein of unknown function (DUF3586) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-D1R / Cysteine protease
Similarity search - Component
Biological speciesTrypanosoma brucei rhodesiense (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBrinen, L.S. / Marion, R.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Vinyl sulfones as antiparasitic agents and a structural basis for drug design.
Authors: Kerr, I.D. / Lee, J.H. / Farady, C.J. / Marion, R. / Rickert, M. / Sajid, M. / Pandey, K.C. / Caffrey, C.R. / Legac, J. / Hansell, E. / McKerrow, J.H. / Craik, C.S. / Rosenthal, P.J. / Brinen, L.S.
History
DepositionMar 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4802
Polymers22,9031
Non-polymers5771
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.377, 39.716, 39.566
Angle α, β, γ (deg.)120.38, 93.89, 101.18
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cysteine protease


Mass: 22903.188 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei rhodesiense (eukaryote)
Species: Trypanosoma brucei / Strain: rhodesiense / Gene: rhodesain / Plasmid: pPIC Z / Production host: Pichia pastoris (fungus) / References: UniProt: Q95PM0
#2: Chemical ChemComp-D1R / NALPHA-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]-N-{(1S)-3-PHENYL-1-[2-(PHENYLSULFONYL)ETHYL]PROPYL}-L-PHENYLALANINAMIDE


Mass: 576.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H40N4O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.0 M Sodium citrate; imidazole pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 15, 2000 / Details: MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 18751 / % possible obs: 89.7 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.047
Reflection shellResolution: 1.65→1.7 Å / Rmerge(I) obs: 0.147 / % possible all: 83.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F2A WITHOUT INHIBITOR OR WATERS, WITH SIDE CHAINS THAT DIFFER CUT BACK TO ALANINE

1f2a


Resolution: 1.65→19.46 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.58 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.175 950 5.1 %RANDOM
Rwork0.135 ---
obs0.137 17747 89.47 %-
all-51956 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.17 Å20.51 Å2
2---0.41 Å20.28 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1626 0 41 169 1836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211714
X-RAY DIFFRACTIONr_bond_other_d0.0030.021081
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9512342
X-RAY DIFFRACTIONr_angle_other_deg1.6653.0052656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6715220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.84326.70979
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81215249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.611152
X-RAY DIFFRACTIONr_chiral_restr0.110.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02325
X-RAY DIFFRACTIONr_nbd_refined0.2090.2350
X-RAY DIFFRACTIONr_nbd_other0.1930.21115
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2847
X-RAY DIFFRACTIONr_nbtor_other0.0940.2812
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5431.51369
X-RAY DIFFRACTIONr_mcbond_other0.3441.5450
X-RAY DIFFRACTIONr_mcangle_it1.90421712
X-RAY DIFFRACTIONr_scbond_it3.173768
X-RAY DIFFRACTIONr_scangle_it4.5934.5627
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 70 -
Rwork0.199 1211 -
obs--83.51 %

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