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- PDB-4lp9: Endothiapepsin complexed with Phe-reduced-Tyr peptide. -

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Basic information

Entry
Database: PDB / ID: 4lp9
TitleEndothiapepsin complexed with Phe-reduced-Tyr peptide.
Components
  • Endothiapepsin
  • Ser-Leu-Phe-His-Phenylalanyl-reduced-peptide-bond-Tyrosyl-Thr-Pro
Keywordshydrolase/hydrolase inhibitor / Aspartic proteinase fold / Proteolysis / HYDROLASE (ACID PROTEINASE) / 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
Ser-Leu-Phe-His-Phenylalanyl-reduced-peptide-bond-Tyrosyl-Thr-Pro / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.35 Å
AuthorsGuo, J. / Cooper, J.B. / Wood, S.P.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: The structure of endothiapepsin complexed with a Phe-Tyr reduced-bond inhibitor at 1.35 angstrom resolution.
Authors: Guo, J. / Cooper, J.B. / Wood, S.P.
History
DepositionJul 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endothiapepsin
I: Ser-Leu-Phe-His-Phenylalanyl-reduced-peptide-bond-Tyrosyl-Thr-Pro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,65311
Polymers34,8122
Non-polymers8419
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-46 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.620, 72.787, 45.113
Angle α, β, γ (deg.)90.00, 108.54, 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: Protein/peptide Ser-Leu-Phe-His-Phenylalanyl-reduced-peptide-bond-Tyrosyl-Thr-Pro


Type: Peptide-like / Class: Inhibitor / Mass: 998.154 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: Ser-Leu-Phe-His-Phenylalanyl-reduced-peptide-bond-Tyrosyl-Thr-Pro
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 0.1 M sodium acetate, 63% saturated ammonium sulfate, 3 mg/ml enzyme, 2 mM inhibitor (dissolved initially in DMSO), pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0435 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0435 Å / Relative weight: 1
ReflectionResolution: 1.35→28.32 Å / Num. all: 69622 / Num. obs: 69622 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 14.8
Reflection shellResolution: 1.35→1.38 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4381 / Rsym value: 0.571 / % possible all: 84.1

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Processing

Software
NameVersionClassification
GDAdata collection
FFTmodel building
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1GVX

1gvx


Resolution: 1.35→27.72 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.645 / SU ML: 0.029 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1649 3576 5 %RANDOM
Rwork0.1231 ---
obs0.1252 66078 98.42 %-
all-70843 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.182 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.03 Å2
2---0.05 Å20 Å2
3----0 Å2
Refine analyzeLuzzati coordinate error obs: 0.05 Å
Refinement stepCycle: LAST / Resolution: 1.35→27.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 51 335 2847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022555
X-RAY DIFFRACTIONr_bond_other_d0.0040.022291
X-RAY DIFFRACTIONr_angle_refined_deg2.1121.9653460
X-RAY DIFFRACTIONr_angle_other_deg1.0183.0045292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.02824.64384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.0215345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.079152
X-RAY DIFFRACTIONr_chiral_restr0.1290.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212795
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02551
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0591.2461331
X-RAY DIFFRACTIONr_mcbond_other1.9521.2431330
X-RAY DIFFRACTIONr_mcangle_it2.4661.881634
X-RAY DIFFRACTIONr_mcangle_other2.4721.8811635
X-RAY DIFFRACTIONr_scbond_it3.8141.5971224
X-RAY DIFFRACTIONr_scbond_other3.8081.5961224
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0112.251827
X-RAY DIFFRACTIONr_long_range_B_refined5.36312.723105
X-RAY DIFFRACTIONr_long_range_B_other5.35112.7173105
X-RAY DIFFRACTIONr_rigid_bond_restr5.69834846
X-RAY DIFFRACTIONr_sphericity_free42.1925138
X-RAY DIFFRACTIONr_sphericity_bonded12.40655008
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 233 -
Rwork0.386 4318 -
obs-4551 87.37 %

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