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- PDB-2p86: The high resolution crystal structure of rhodesain, the major cat... -

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Basic information

Entry
Database: PDB / ID: 2p86
TitleThe high resolution crystal structure of rhodesain, the major cathepsin L protease from T. brucei rhodesiense, bound to inhibitor K11002
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-VS1 / Cysteine protease
Similarity search - Component
Biological speciesTrypanosoma brucei rhodesiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsBrinen, L.S. / Marion, R.
CitationJournal: To be Published
Title: THE high resolution structure of rhodesain, the major cathepsin L protease from trypanosoma brucei rhodesiense, illustrates the basis for differences in inhibition profiles from other papain ...Title: THE high resolution structure of rhodesain, the major cathepsin L protease from trypanosoma brucei rhodesiense, illustrates the basis for differences in inhibition profiles from other papain family cysteine proteases
Authors: Marion, R. / Hansell, E. / Caffrey, C. / Roush, W.R. / Brinen, L.S.
History
DepositionMar 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 24, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Oct 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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 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)24,15013
Polymers22,9031
Non-polymers1,24612
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.659, 78.628, 80.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cysteine protease


Mass: 22903.188 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: Ser to Ala mutation at 172
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, cathepsin L
#2: Chemical ChemComp-VS1 / 3-[[N-[MORPHOLIN-N-YL]-CARBONYL]-PHENYLALANINYL-AMINO]-5- PHENYL-PENTANE-1-SULFONYLBENZENE


Mass: 563.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H37N3O5S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 298 K / pH: 9
Details: 1.6M Ammonium Sulfate, 0.1 M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2005 / Details: FLAT MIRROR, RH COATED
RadiationMonochromator: SIDE-SCATTERING CUBEROOT I- BEAM BEND SINGLE CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.16→40.36 Å / Num. obs: 68633 / % possible obs: 91.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 27.2
Reflection shellResolution: 1.16→1.22 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 14.9 / % possible all: 80

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P7U, WITHOUT WATERS OR SMALL MOLECULE INHIBITOR

2p7u


Resolution: 1.16→40.36 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.603 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13 3463 5 %RANDOM
Rwork0.11 ---
obs0.111 65123 91.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.799 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.16→40.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 93 402 2135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221775
X-RAY DIFFRACTIONr_bond_other_d0.0020.021154
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.9652413
X-RAY DIFFRACTIONr_angle_other_deg1.5683.012772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.12326.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37515250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.184152
X-RAY DIFFRACTIONr_chiral_restr0.120.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02317
X-RAY DIFFRACTIONr_nbd_refined0.2230.2396
X-RAY DIFFRACTIONr_nbd_other0.2010.21354
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2879
X-RAY DIFFRACTIONr_nbtor_other0.1020.2837
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2258
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2540.218
X-RAY DIFFRACTIONr_metal_ion_refined0.3180.239
X-RAY DIFFRACTIONr_metal_ion_other0.2260.238
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3390.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6541.51396
X-RAY DIFFRACTIONr_mcbond_other0.8441.5455
X-RAY DIFFRACTIONr_mcangle_it2.39321737
X-RAY DIFFRACTIONr_scbond_it3.4123821
X-RAY DIFFRACTIONr_scangle_it4.3534.5668
X-RAY DIFFRACTIONr_rigid_bond_restr1.65433663
X-RAY DIFFRACTIONr_sphericity_free9.9723403
X-RAY DIFFRACTIONr_sphericity_bonded4.30832887
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.134 187 -
Rwork0.094 3568 -
obs--68.56 %

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