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- PDB-1e82: Endothiapepsin complex with renin inhibitor MERCK-KGAA-EMD59601 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1.0E+82
TitleEndothiapepsin complex with renin inhibitor MERCK-KGAA-EMD59601
ComponentsENDOTHIAPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
Chem-M90 / Endothiapepsin
Similarity search - Component
Biological speciesENDOTHIA PARASITICA (chestnut blight fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsRead, J.A. / Cooper, J.B. / Toldo, L. / Rippmann, F. / Raddatz, P.
CitationJournal: Thesis / Year: 1999
Title: Refinement of Four Endothiapepsin Inhibitor Complexes. Crystallographic Studies of Cytochrome Ch from Methylobacterium Extorquens and Inhibitor Complexes of Aspartic Proteinases.
Authors: Read, J.A.
History
DepositionSep 15, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2000Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: BASED ON SUBMISSION 4APE
Remark 700 SHEET DETERMINATION METHOD: BASED ON SUBMISSION 4APE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: ENDOTHIAPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4702
Polymers33,8141
Non-polymers6561
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.870, 74.120, 45.840
Angle α, β, γ (deg.)90.00, 110.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOTHIAPEPSIN /


Mass: 33813.855 Da / Num. of mol.: 1 / Fragment: RESIDUES 90-419 / Source method: isolated from a natural source
Source: (natural) ENDOTHIA PARASITICA (chestnut blight fungus)
References: UniProt: P11838, mucorpepsin
#2: Chemical ChemComp-M90 / (2S)-1-{[(2R)-1-{[(2S,3R)-1-cyclohexyl-3-hydroxy-4-(pyridin-4-yloxy)butan-2-yl]amino}-3-(methylsulfanyl)-1-oxopropan-2-yl]amino}-1-oxo-3-phenylpropan-2-yl 4-aminopiperidine-1-carboxylate


Type: peptide-like / Mass: 655.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H49N5O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growpH: 5
Details: BATCH METHOD PROTEIN: 10MG/ML, 50 MM AMMONIUM ACETATE PH 5.0, ~2.2 M AMMONIUM SULPHATE, 1% ACETONE. INHIBITOR WAS ADDED IN A 10:1 STOICHIOMETRIC RATIO.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 26434 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.092 / Net I/σ(I): 5.4
Reflection shellResolution: 1.9→2.1 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.263 / % possible all: 85.5

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4APE

4ape


Resolution: 2.05→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.237 -5 %
Rwork0.181 --
obs-21510 98.9 %
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 46 132 2567

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