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- PDB-6scv: Endothiapepsin in complex with ligand 69 -

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Basic information

Entry
Database: PDB / ID: 6scv
TitleEndothiapepsin in complex with ligand 69
ComponentsEndothiapepsin
KeywordsHYDROLASE / Aspartic Proteinase / Endothiapepsin / Complex with tetrazole / Inhibitor
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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Chem-L7K / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMagari, F. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Endothiapepsin in complex with ligand 69
Authors: Magari, F. / Heine, A. / Konstantinidou, M. / Sutanto, F. / Haupenthal, J. / Jumde, R.V. / Unver, M.Y. / Camacho, C.J. / Hirsch, A.K.H. / Doemling, A. / Klebe, G.
History
DepositionJul 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)34,2063
Polymers33,8141
Non-polymers3922
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.283, 73.040, 52.878
Angle α, β, γ (deg.)90.000, 109.378, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-L7K / [(~{R})-cyclohexyl-[1-(2-phenylethyl)-1,2,3,4-tetrazol-5-yl]methyl]diazane


Mass: 300.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24N6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 49.58 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M AMMONIUM ACETATE, 0.1M SODIUM ACETATE, 24-30% PEG 4000 CRYSTAL OBTAINED BY STREAK-SEEDING

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Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 35726 / % possible obs: 99.3 % / Redundancy: 4.4 % / Biso Wilson estimate: 13.9 Å2 / CC1/2: 0.999 / Rsym value: 0.038 / Net I/σ(I): 24.79
Reflection shellResolution: 1.7→1.8 Å / Mean I/σ(I) obs: 6.26 / Num. unique obs: 5629 / CC1/2: 0.947 / Rsym value: 0.224 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.7→39.58 Å / SU ML: 0.1262 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.8521
RfactorNum. reflection% reflection
Rfree0.1644 1785 5 %
Rwork0.1396 --
obs0.1408 35700 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.24 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 28 274 2672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052487
X-RAY DIFFRACTIONf_angle_d0.80263409
X-RAY DIFFRACTIONf_chiral_restr0.0509405
X-RAY DIFFRACTIONf_plane_restr0.0053454
X-RAY DIFFRACTIONf_dihedral_angle_d13.47611426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.24031310.18412486X-RAY DIFFRACTION95.48
1.74-1.790.18551360.14722591X-RAY DIFFRACTION99.78
1.79-1.850.18921380.15342612X-RAY DIFFRACTION99.75
1.85-1.920.17761380.13342629X-RAY DIFFRACTION99.96
1.92-20.19071370.1252599X-RAY DIFFRACTION99.89
2-2.090.1491380.12242614X-RAY DIFFRACTION99.85
2.09-2.20.14181370.11882618X-RAY DIFFRACTION99.93
2.2-2.330.14271380.12622613X-RAY DIFFRACTION99.85
2.33-2.510.15571400.132653X-RAY DIFFRACTION99.89
2.51-2.770.14411360.1372597X-RAY DIFFRACTION99.82
2.77-3.170.16831390.14352627X-RAY DIFFRACTION99.86
3.17-3.990.16791380.152639X-RAY DIFFRACTION99.75
3.99-39.580.1641390.14792637X-RAY DIFFRACTION98.16
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.18630983280.02246349079150.09869835686530.441934283820.0736332559750.266356359325-0.0253643242752-0.04809685220530.03535910812220.0646111542929-0.0191890626825-0.005749882270040.00443776895531-0.0263145397302-0.01811482872820.100193599460.00243406551142-0.005090117406210.103328077686-0.003322594212750.09070538567515.22508782252-6.011960800214.80232376
20.147766424566-0.1187478908520.05360839358320.268023017957-0.1109585256980.141011179393-0.01921583998420.0145194437724-0.000314608364539-0.00111111467759-0.0132780168742-0.0610399475259-0.0199711528816-0.00494991754629-0.0131043069730.0914461082392-0.003445821662960.002971470194220.08646852850010.004095829856460.09526454363382.189034494687.09866804427-4.89281369818
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 183 )
2X-RAY DIFFRACTION2chain 'A' and (resid 184 through 330 )

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