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- PDB-1ewo: THE CYSTEINE PROTEASE CRUZAIN BOUND TO WRR-204 -

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Basic information

Entry
Database: PDB / ID: 1ewo
TitleTHE CYSTEINE PROTEASE CRUZAIN BOUND TO WRR-204
ComponentsCRUZAIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / cysteine protease / drug design / covalent inhibitor / cruzipain / 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-VSC / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsBrinen, L.S. / Gillmor, S.A. / Fletterick, R.J.
Citation
Journal: To be Published
Title: Crystal Structure of Cruzain bound to WRR-204
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

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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)23,3162
Polymers22,7151
Non-polymers6011
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.206, 51.551, 45.511
Angle α, β, γ (deg.)90.00, 116.13, 90.00
Int Tables number4
Space group name H-MP1211

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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-VSC / N-[N'-BENZYLOXYCARBONYL-PHENYLALANINYL]-3-AMINO-5-PHENYL-PENTANE-1-SULFONIC ACID PHENYL ESTER / WRR-204


Type: peptide-like / Mass: 600.724 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H36N2O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsVSC WAS N-[N'-BENZYLOXYCARBONYL-PHENYLALANINYL]-3-AMINO- 5-PHENYL-PENT-1-ENE-1-SULFONIC ACID PHENYL ...VSC WAS N-[N'-BENZYLOXYCARBONYL-PHENYLALANINYL]-3-AMINO- 5-PHENYL-PENT-1-ENE-1-SULFONIC ACID PHENYL ESTER BEFORE REACTION WITH THE PROTEASE. AFTER REACTION, THE SG OF CYS 25 IS LINKED TO C32 OF THE VSC 280, N-[N'-BENZYLOXYCARBONYL-PHENYLALANINYL]-3-AMINO-5- PHENYL-PENTANE-1-SULFONIC ACID PHENYL ESTER. THE PHENYL RING ATTACHED TO ONE OXYGEN OF THE SULFONIC ACID PORTION OF THE LIGAND IS MISSING IN THE DENSITY.
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: 2.1 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.8M NaCitrate, pH 7.0, 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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 14, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 10544 / Num. obs: 10544 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 7.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.197 / Num. unique all: 997 / % possible all: 90.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.843refinement
RefinementResolution: 2.1→30 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: parameters for VSC from moloc
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1033 9.8 %RANDOM
Rwork0.221 ---
all0.23 10544 --
obs0.221 10544 95 %-
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 37 38 1668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_improper_angle_d1.04
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.355 166 9.8 %
Rwork0.298 1522 -
obs--91.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3VSC.TPX
X-RAY DIFFRACTION4VSC_VER2.TPX

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