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- PDB-4lap: Endothiapepsin in complex with thiophen-based inhibitor SAP114 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4lap
TitleEndothiapepsin in complex with thiophen-based inhibitor SAP114
ComponentsEndothiapepsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ASPARTATE PROTEASE / Inhibitor Complex / 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-1VT / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsPark, A. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Endothiapepsin in Complex with Thiophen based Inhibitors
Authors: Kuhnert, M. / Park, A. / Heine, A. / Klebe, G. / Diederich, W.E.
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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)34,4544
Polymers33,8141
Non-polymers6403
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.419, 73.064, 52.752
Angle α, β, γ (deg.)90.00, 109.68, 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 / Fragment: UNP residues 90-419 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Chemical ChemComp-1VT / N-benzyl-2-[(N-benzyl-beta-alanyl)amino]-4-phenylthiophene-3-carboxamide


Mass: 469.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H27N3O2S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 49.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M NH4AC, 0.1M ACETATE-BUFFER, 26% PEG4000, , pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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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: Dec 11, 2011
RadiationMonochromator: Si-111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.12→30 Å / Num. all: 119175 / Num. obs: 119175 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.045 / Net I/σ(I): 30.2
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 5702 / Rsym value: 0.421 / % possible all: 92.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→17.623 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 12.01 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1444 5978 5.02 %random
Rwork0.129 ---
obs0.1298 119169 95.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.12→17.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 44 321 2735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122561
X-RAY DIFFRACTIONf_angle_d1.5633523
X-RAY DIFFRACTIONf_dihedral_angle_d13.694840
X-RAY DIFFRACTIONf_chiral_restr0.094412
X-RAY DIFFRACTIONf_plane_restr0.009455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.13260.17531800.16953534X-RAY DIFFRACTION90
1.1326-1.14590.18651960.15643700X-RAY DIFFRACTION94
1.1459-1.15990.17011880.14433628X-RAY DIFFRACTION93
1.1599-1.17460.15412070.13643662X-RAY DIFFRACTION94
1.1746-1.190.15981790.1313708X-RAY DIFFRACTION94
1.19-1.20630.14471640.12363733X-RAY DIFFRACTION94
1.2063-1.22350.15461980.12373684X-RAY DIFFRACTION94
1.2235-1.24180.15141990.12553704X-RAY DIFFRACTION95
1.2418-1.26120.15052110.12053757X-RAY DIFFRACTION95
1.2612-1.28190.15741840.11953689X-RAY DIFFRACTION95
1.2819-1.3040.14232190.11713729X-RAY DIFFRACTION95
1.304-1.32770.12511940.10883741X-RAY DIFFRACTION95
1.3277-1.35320.13462070.10263735X-RAY DIFFRACTION96
1.3532-1.38080.13222060.09953789X-RAY DIFFRACTION96
1.3808-1.41080.12972000.09773761X-RAY DIFFRACTION96
1.4108-1.44360.13071820.09873754X-RAY DIFFRACTION96
1.4436-1.47970.11931930.09733793X-RAY DIFFRACTION96
1.4797-1.51970.13452260.09583793X-RAY DIFFRACTION96
1.5197-1.56440.12252220.09123797X-RAY DIFFRACTION97
1.5644-1.61480.11752090.09513803X-RAY DIFFRACTION97
1.6148-1.67250.1192040.10073828X-RAY DIFFRACTION97
1.6725-1.73940.12231970.10863860X-RAY DIFFRACTION98
1.7394-1.81850.12521850.11373892X-RAY DIFFRACTION98
1.8185-1.91430.14392050.12063846X-RAY DIFFRACTION98
1.9143-2.0340.1332160.11973856X-RAY DIFFRACTION98
2.034-2.19080.13432150.12343896X-RAY DIFFRACTION99
2.1908-2.41080.15532250.1343881X-RAY DIFFRACTION99
2.4108-2.75850.15261910.14733923X-RAY DIFFRACTION99
2.7585-3.47110.15831880.15343975X-RAY DIFFRACTION99
3.4711-17.62540.16451880.16183740X-RAY DIFFRACTION93

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