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- PDB-3uri: Endothiapepsin-DB5 complex. -

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Basic information

Entry
Database: PDB / ID: 3uri
TitleEndothiapepsin-DB5 complex.
Components
  • DB5 peptide
  • Endothiapepsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / hydrolase-hydrolase inhibitor complex / aspartic proteinase mechanism / transition state analogue.
Function / homology
Function and homology information


endothiapepsin / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DB5 peptide / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsBailey, D. / Sanz-Aparicio, J. / Albert, A. / Cooper, J.B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: An analysis of subdomain orientation, conformational change and disorder in relation to crystal packing of aspartic proteinases.
Authors: Bailey, D. / Carpenter, E.P. / Coker, A. / Coker, S. / Read, J. / Jones, A.T. / Erskine, P. / Aguilar, C.F. / Badasso, M. / Toldo, L. / Rippmann, F. / Sanz-Aparicio, J. / Albert, A. / ...Authors: Bailey, D. / Carpenter, E.P. / Coker, A. / Coker, S. / Read, J. / Jones, A.T. / Erskine, P. / Aguilar, C.F. / Badasso, M. / Toldo, L. / Rippmann, F. / Sanz-Aparicio, J. / Albert, A. / Blundell, T.L. / Roberts, N.B. / Wood, S.P. / Cooper, J.B.
History
DepositionNov 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2May 9, 2012Group: Database references
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Dec 16, 2015Group: Atomic model
Revision 1.5Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 999ASP A54 AND GLY A55 HAVE CYCLIZED TO FORM A SUCCINIMIDE, SUI A54.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endothiapepsin
B: DB5 peptide


Theoretical massNumber of molelcules
Total (without water)34,8612
Polymers34,8612
Non-polymers00
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-11 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.020, 75.560, 42.800
Angle α, β, γ (deg.)90.00, 97.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endothiapepsin / / Aspartate protease


Mass: 33795.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Protein/peptide DB5 peptide


Type: Peptide-like / Class: Enzyme inhibitor / Mass: 1065.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: DB5 peptide
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 298 K / Method: batch method / pH: 4.5
Details: 0.1M acetate buffer. 10-fold molar excess of inhibitor DB5 over enzyme. Enzyme concentration 2 mg/ml. 2.2M ammonium sulphate. , pH 4.5, Batch method, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.54178 Å
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER / Date: Jan 1, 1991
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. all: 17168 / Num. obs: 10301 / % possible obs: 60 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.15

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
FFTmodel building
SHELXL-97refinement
Cadraldata reduction
ROTAVATAAgrovatadata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: AUTHOR STATES THAT THE DATA ARE ONLY ABOUT 60% COMPLETE AS IT IS A VERY OLD DATASET THAT WAS COLLECTED ON A DIFFRACTOMETER AND THE CRYSTAL DIED BEFORE THE DATA COLLECTION WAS COMPLETED
RfactorNum. reflectionSelection details
Rfree0.2527 482 Random
Rwork0.1485 --
all0.1485 10301 -
obs0.1485 9712 -
Refine analyzeLuzzati coordinate error obs: 0.178 Å
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2453 0 0 289 2742
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.022

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