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- PDB-5dr7: Endothiapepsin in complex with fragment 311 -

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Basic information

Entry
Database: PDB / ID: 5dr7
TitleEndothiapepsin in complex with fragment 311
ComponentsEndothiapepsin
KeywordsHYDROLASE / fragment screening / 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
Chem-5HJ / ACETATE ION / TRIETHYLENE GLYCOL / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.234 Å
AuthorsHeine, A. / Schiebel, J. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
BMBF05K13RM1 Germany
Citation
Journal: To Be Published
Title: Crystallographic Fragment Screening of an Entire Library
Authors: Heine, A. / Schiebel, J. / 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
DepositionSep 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 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 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7339
Polymers33,8141
Non-polymers9198
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint4 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.343, 73.124, 52.770
Angle α, β, γ (deg.)90.00, 109.44, 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 / Fragment: UNP residues 90-419 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin

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Non-polymers , 5 types, 297 molecules

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-5HJ / (2R)-3-cyclopropyl-2-(4-methoxyphenyl)-1,3-thiazolidin-4-one


Mass: 249.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15NO2S
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: 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: 2.44 Å3/Da / Density % sol: 49.58 %
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: 14.3 / Wavelength: 0.895 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895 Å / Relative weight: 1
ReflectionResolution: 1.23→42.8 Å / Num. obs: 89949 / % possible obs: 96.5 % / Redundancy: 4.2 % / Rsym value: 0.096 / Net I/σ(I): 11.9
Reflection shellResolution: 1.23→1.31 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 3.3 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1492refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PCW

3pcw


Resolution: 1.234→25.511 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1449 4497 5 %random selection
Rwork0.1229 ---
obs0.124 89927 96.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.234→25.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 61 289 2718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092558
X-RAY DIFFRACTIONf_angle_d1.3283508
X-RAY DIFFRACTIONf_dihedral_angle_d10.946846
X-RAY DIFFRACTIONf_chiral_restr0.078410
X-RAY DIFFRACTIONf_plane_restr0.008460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.234-1.2480.2385950.20671794X-RAY DIFFRACTION61
1.248-1.26270.17411490.16322844X-RAY DIFFRACTION96
1.2627-1.27810.1921470.1562778X-RAY DIFFRACTION96
1.2781-1.29430.19461520.1472890X-RAY DIFFRACTION97
1.2943-1.31130.14731470.14062789X-RAY DIFFRACTION96
1.3113-1.32920.16961500.13442865X-RAY DIFFRACTION97
1.3292-1.34820.1441500.13262836X-RAY DIFFRACTION97
1.3482-1.36840.16831510.1282869X-RAY DIFFRACTION97
1.3684-1.38970.14811500.12022866X-RAY DIFFRACTION97
1.3897-1.41250.15061480.1182809X-RAY DIFFRACTION97
1.4125-1.43690.14521510.11072855X-RAY DIFFRACTION97
1.4369-1.4630.14861520.10552904X-RAY DIFFRACTION97
1.463-1.49110.12321500.10332840X-RAY DIFFRACTION98
1.4911-1.52160.12451510.10132875X-RAY DIFFRACTION98
1.5216-1.55460.121540.10012924X-RAY DIFFRACTION98
1.5546-1.59080.11821510.09492858X-RAY DIFFRACTION98
1.5908-1.63060.12631520.09452895X-RAY DIFFRACTION98
1.6306-1.67470.13451530.09652901X-RAY DIFFRACTION98
1.6747-1.72390.12951520.09782900X-RAY DIFFRACTION99
1.7239-1.77960.12881530.10242894X-RAY DIFFRACTION98
1.7796-1.84310.14531520.10372901X-RAY DIFFRACTION99
1.8431-1.91690.14041540.10592913X-RAY DIFFRACTION98
1.9169-2.00410.12891520.10322891X-RAY DIFFRACTION98
2.0041-2.10970.12421530.10242913X-RAY DIFFRACTION98
2.1097-2.24190.12621530.10692896X-RAY DIFFRACTION99
2.2419-2.41480.13151540.11772929X-RAY DIFFRACTION99
2.4148-2.65760.14171540.12432925X-RAY DIFFRACTION99
2.6576-3.04160.15681550.13542948X-RAY DIFFRACTION99
3.0416-3.83010.15161560.14222962X-RAY DIFFRACTION99
3.8301-25.51590.16681560.162966X-RAY DIFFRACTION98

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