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- PDB-1ewm: THE CYSTEINE PROTEASE CRUZAIN BOUND TO WRR-112 -

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Basic information

Entry
Database: PDB / ID: 1ewm
TitleTHE CYSTEINE PROTEASE CRUZAIN BOUND TO WRR-112
ComponentsCRUZAIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / cruzain / cruzipain / drug design / covalent inhibitor / cysteine protease / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


cruzipain / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-RL2 / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBrinen, L.S. / Gillmor, S.A. / Fletterick, R.J.
Citation
Journal: To be Published
Title: Crystal Structure of Cruzain bound to WRR-112
Authors: Brinen, L.S. / Gillmor, S.A. / Fletterick, R.J.
#1: Journal: Enzyme-ligand Interactions, Inhibition and Specificity
Year: 1998
Title: Chapter 3: X-ray Structures of Complexes of Cruzain with Designed Covalent Inhibitors
Authors: Gillmor, S.A.
#2: Journal: Protein Sci. / Year: 1997
Title: Structural Determinants of Specificity in the Cysteine Protease Cruzain
Authors: Gillmor, S.A. / Craik, C.S. / Fletterick, R.J.
#3: Journal: J.Mol.Biol. / Year: 1995
Title: The Crystal Structure of Cruzain: a Therapeutic Target for Chagas' Disease
Authors: McGrath, M.E. / Eakin, A.E. / Engel, J.C. / McKerrow, J.H. / Craik, C.S. / Fletterick, R.J.
History
DepositionApr 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: CRUZAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0802
Polymers22,7151
Non-polymers3641
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.258, 51.700, 45.271
Angle α, β, γ (deg.)90.00, 115.20, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe biological assembly is the monomer found in the asymmetric unit

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Components

#1: Protein CRUZAIN / cruzipain / cruzaine


Mass: 22715.133 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: CHEY / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA
References: UniProt: P25779, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-RL2 / N-[3-CARBOXY-2-HYDROXY-PROPIONYL]-L-HOMOPHENYLALANYL-AMINO-2-METHYLBUTANE / WRR-112


Type: peptide-like / Mass: 364.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28N2O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsRL2 IS AN E-64 ANALOG. RL2 WAS N-(3-CARBOXYOXIRANE-2-CARBONYL)-L- HOMOPHENYLALANYL-AMINO-2- ...RL2 IS AN E-64 ANALOG. RL2 WAS N-(3-CARBOXYOXIRANE-2-CARBONYL)-L- HOMOPHENYLALANYL-AMINO-2-METHYLBUTANE BEFORE REACTION WITH THE PROTEASE. DURING REACTION WITH THE PROTEASE, THE EPOXIDE RING OPENS TO FORM N-[3-CARBOXY-2-HYDROXY- PROPIONYL]-L-HOMOPHENYLALANYL-AMINO-2-METHYLBUTANE. THE SG OF CYS 25 IS THEN LINKED TO THE C2 OF RL2 280 AFTER REACTION.
Sequence detailsTHERE IS A STOP CODON AFTER RESIDUE 212.

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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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.9M NaCitrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 18, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 11831 / Num. obs: 11831 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.75 % / Biso Wilson estimate: 5.5 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 6
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.167 / Num. unique all: 1139 / % possible all: 91.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.843refinement
RefinementResolution: 2→25 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: toph19 and param19
RfactorNum. reflection% reflectionSelection details
Rfree0.206 570 4.8 %RANDOM
Rwork0.173 ---
all0.18 11819 --
obs0.173 11819 95.8 %-
Displacement parametersBiso mean: 10.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 26 57 1676
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_dihedral_angle_d25.9
X-RAY DIFFRACTIONx_improper_angle_d0.94
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 82 4.4 %
Rwork0.209 1790 -
obs--92.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19SG.PROTOHP19SG2.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3INHIB112.TPX
X-RAY DIFFRACTION4EPOX.TPX

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