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- PDB-3hd3: High resolution crystal structure of cruzain bound to the vinyl s... -

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Basic information

Entry
Database: PDB / ID: 3hd3
TitleHigh resolution crystal structure of cruzain bound to the vinyl sulfone inhibitor SMDC-256047
ComponentsCruzipain
KeywordsHYDROLASE / cysteine protease / Autocatalytic cleavage / Disulfide bond / Glycoprotein / Protease / Thiol protease / Zymogen
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-25B / ETHANOL / DI(HYDROXYETHYL)ETHER / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKerr, I.D. / Debnath, M. / Brinen, L.S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Novel non-peptidic vinylsulfones targeting the S2 and S3 subsites of parasite cysteine proteases.
Authors: Bryant, C. / Kerr, I.D. / Debnath, M. / Ang, K.K. / Ratnam, J. / Ferreira, R.S. / Jaishankar, P. / Zhao, D. / Arkin, M.R. / McKerrow, J.H. / Brinen, L.S. / Renslo, A.R.
History
DepositionMay 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cruzipain
B: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,82510
Polymers45,3382
Non-polymers1,4878
Water7,116395
1
A: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4846
Polymers22,6691
Non-polymers8145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3414
Polymers22,6691
Non-polymers6723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.687, 72.493, 60.930
Angle α, β, γ (deg.)90.00, 89.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cruzipain / Cruzaine / Major cysteine proteinase


Mass: 22669.105 Da / Num. of mol.: 2 / Fragment: cruzain mature domain / Mutation: S49A, S172G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: cruzain / Plasmid: pPICZalphaB / Production host: Pichia pastoris (fungus) / References: UniProt: P25779, cruzipain

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Non-polymers , 6 types, 403 molecules

#2: Chemical ChemComp-25B / (1R,2R)-2-[(4-chlorophenyl)carbonyl]-N-{(1S)-1-[2-(phenylsulfonyl)ethyl]pentyl}cyclohexanecarboxamide / (1R,2R)-2-(4-chlorobenzoyl)-N-((S,E)-1-(phenylsulfonyl)hept-1-en-3-yl)cyclohexanecarboxamide


Mass: 504.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H34ClNO4S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Sodium HEPES pH 7.5, 2% PEG 400, 2.0M Ammonium sulfate, 30% Ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2008 / Details: Vertical focusing mirror
RadiationMonochromator: single crystal (Si111) bent monochromator (horizontal focusing).
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→72.5 Å / Num. all: 38177 / Num. obs: 38177 / % possible obs: 97.3 % / Redundancy: 7.4 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 25
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 12 / Num. unique all: 5147 / % possible all: 90

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0071refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→60.93 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.502 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17636 1918 5 %RANDOM
Rwork0.14297 ---
obs0.14469 36240 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 4.456 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20.04 Å2
2---0.01 Å20 Å2
3----0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.101 Å0.106 Å
Refinement stepCycle: LAST / Resolution: 1.75→60.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 98 395 3668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213362
X-RAY DIFFRACTIONr_bond_other_d0.0010.022120
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9414593
X-RAY DIFFRACTIONr_angle_other_deg0.9763.0055176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1375429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6425.735136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.26815459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.45156
X-RAY DIFFRACTIONr_chiral_restr0.10.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213812
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02646
X-RAY DIFFRACTIONr_mcbond_it0.8641.52117
X-RAY DIFFRACTIONr_mcbond_other0.2841.5889
X-RAY DIFFRACTIONr_mcangle_it1.35523379
X-RAY DIFFRACTIONr_scbond_it2.23831245
X-RAY DIFFRACTIONr_scangle_it3.5154.51213
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 121 -
Rwork0.163 2271 -
obs--82.09 %
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)
10.81260.3509-0.06780.6087-0.04120.25470.0188-0.03270.0020.0206-0.02030.0073-0.00580.00980.00150.0041-0.0013-0.01340.003300.057415.383-0.1063.54
20.42480.38890.37370.82710.54031.1296-0.01950.0222-0.0044-0.00340.04050.0094-0.02170.0899-0.0210.0027-0.0009-0.00630.01230.00340.05515.905-10.81933.134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 215
2X-RAY DIFFRACTION2B1 - 215

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