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- PDB-3pmu: Endothiapepsin in complex with a fragment -

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Basic information

Entry
Database: PDB / ID: 3pmu
TitleEndothiapepsin in complex with a fragment
ComponentsEndothiapepsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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-F7L / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsKoester, H. / Heine, A. / Klebe, G.
CitationJournal: J.Med.Chem. / Year: 2011
Title: A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes.
Authors: Koster, H. / Craan, T. / Brass, S. / Herhaus, C. / Zentgraf, M. / Neumann, L. / Heine, A. / Klebe, G.
History
DepositionNov 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2May 31, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0672
Polymers33,8141
Non-polymers2531
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.190, 73.740, 52.480
Angle α, β, γ (deg.)90.00, 109.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endothiapepsin / Aspartate protease


Mass: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Chemical ChemComp-F7L / (2S)-1-[(2-fluorobenzyl)oxy]-3-(pyrrolidin-1-yl)propan-2-ol


Mass: 253.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20FNO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M NH4Ac, 0.1M Acetate Buffer pH 4.6, 26% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 25, 2010 / Details: mirrors
RadiationMonochromator: Double Crystal Monochromator KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.43→20 Å / Num. all: 59547 / Num. obs: 59547 / % possible obs: 100 % / Redundancy: 3.1 % / Rsym value: 0.073 / Net I/σ(I): 14.3
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2958 / Rsym value: 0.429 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OEW

1oew


Resolution: 1.43→19.698 Å / SU ML: 0.17 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1887 2856 5.05 %Random
Rwork0.1649 ---
obs0.1661 56527 94.3 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.403 Å2 / ksol: 0.441 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6355 Å20 Å2-3.0426 Å2
2--0.2666 Å2-0 Å2
3---1.3688 Å2
Refinement stepCycle: LAST / Resolution: 1.43→19.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 18 264 2651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052463
X-RAY DIFFRACTIONf_angle_d1.073381
X-RAY DIFFRACTIONf_dihedral_angle_d11.117806
X-RAY DIFFRACTIONf_chiral_restr0.069405
X-RAY DIFFRACTIONf_plane_restr0.005429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.48110.28192300.23824795X-RAY DIFFRACTION85
1.4811-1.54040.22742770.19785087X-RAY DIFFRACTION89
1.5404-1.61050.2162930.17595188X-RAY DIFFRACTION92
1.6105-1.69530.19462720.16065355X-RAY DIFFRACTION94
1.6953-1.80150.18112720.15015411X-RAY DIFFRACTION95
1.8015-1.94050.17172910.155459X-RAY DIFFRACTION96
1.9405-2.13550.16663130.14555572X-RAY DIFFRACTION99
2.1355-2.44410.18893000.1575644X-RAY DIFFRACTION99
2.4441-3.07740.20293260.16995597X-RAY DIFFRACTION98
3.0774-19.70030.17452820.16755563X-RAY DIFFRACTION96

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