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- PDB-4y3t: Endothiapepsin in complex with fragment 207 -

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Basic information

Entry
Database: PDB / ID: 4y3t
TitleEndothiapepsin in complex with fragment 207
ComponentsEndothiapepsin
KeywordsHYDROLASE / fragment screening / aspartic protease / inhibition
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
(3S)-piperidin-3-yl(piperidin-1-yl)methanone / (3R)-piperidin-3-yl(piperidin-1-yl)methanone / ACETATE ION / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsEhrmann, F.R. / Huschmann, F.U. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
BMBF05K13RM1 Germany
Citation
Journal: To Be Published
Title: Crystallographic Fragment Sreening of an Entire Library
Authors: Ehrmann, F.R. / Heine, A. / Klebe, G.
#1: Journal: 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: Koester, H. / Craan, T. / Brass, S. / Herhaus, C. / Zentgraf, M. / Neumann, L. / Heine, A. / Klebe, G.
History
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 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)35,60119
Polymers33,8141
Non-polymers1,78718
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint8 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.320, 72.924, 52.594
Angle α, β, γ (deg.)90.00, 109.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 307 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-46J / (3R)-piperidin-3-yl(piperidin-1-yl)methanone


Mass: 196.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N2O
#6: Chemical ChemComp-46H / (3S)-piperidin-3-yl(piperidin-1-yl)methanone


Mass: 196.289 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20N2O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 35.08 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000. Crystals obtained by streak-seeding

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.42→42.759 Å / Num. obs: 60833 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.07 / Net I/σ(I): 14.33
Reflection shellResolution: 1.42→1.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.99 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIXdev_1779refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PCW

3pcw


Resolution: 1.42→39.507 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1502 3042 5 %random selection
Rwork0.1168 ---
obs0.1184 60831 99.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→39.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 108 289 2772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072606
X-RAY DIFFRACTIONf_angle_d1.2163562
X-RAY DIFFRACTIONf_dihedral_angle_d10.792875
X-RAY DIFFRACTIONf_chiral_restr0.069414
X-RAY DIFFRACTIONf_plane_restr0.006456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4162-1.43830.22371160.16392202X-RAY DIFFRACTION84
1.4383-1.46190.21361400.15512668X-RAY DIFFRACTION100
1.4619-1.48710.20161370.14992604X-RAY DIFFRACTION100
1.4871-1.51420.16881380.13862626X-RAY DIFFRACTION100
1.5142-1.54330.20521400.13362645X-RAY DIFFRACTION100
1.5433-1.57480.16621380.12312630X-RAY DIFFRACTION100
1.5748-1.6090.17761400.1152649X-RAY DIFFRACTION100
1.609-1.64650.1671370.10832620X-RAY DIFFRACTION100
1.6465-1.68760.13861400.10312658X-RAY DIFFRACTION100
1.6876-1.73330.14481390.10252643X-RAY DIFFRACTION100
1.7333-1.78430.15241390.09922631X-RAY DIFFRACTION100
1.7843-1.84190.15691390.09652633X-RAY DIFFRACTION100
1.8419-1.90770.12511400.09412665X-RAY DIFFRACTION100
1.9077-1.98410.12731370.08852608X-RAY DIFFRACTION100
1.9841-2.07440.12321400.08712660X-RAY DIFFRACTION100
2.0744-2.18370.12121400.08722656X-RAY DIFFRACTION100
2.1837-2.32050.11661390.09572638X-RAY DIFFRACTION100
2.3205-2.49970.14521400.10332673X-RAY DIFFRACTION100
2.4997-2.75120.1531390.11092631X-RAY DIFFRACTION100
2.7512-3.14910.13311400.11782662X-RAY DIFFRACTION100
3.1491-3.9670.14751400.12992668X-RAY DIFFRACTION100
3.967-39.52250.16851440.16052719X-RAY DIFFRACTION100

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