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- PDB-1gvw: Endothiapepsin complex with PD-130,328 -

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Basic information

Entry
Database: PDB / ID: 1gvw
TitleEndothiapepsin complex with PD-130,328
ComponentsENDOTHIAPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / ASPARTIC PROTEINASE MECHANISM / TETRAHEDRAL INTERMEDIATE / 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
N-(tert-butoxycarbonyl)-L-phenylalanyl-N-{(1S)-1-[(R)-hydroxy(2-{[(2S)-2-methylbutyl]amino}-2-oxoethyl)phosphoryl]-3- methylbutyl}-3-(1H-imidazol-3-ium-4-yl)-L-alaninamide / Chem-0EM / Endothiapepsin
Similarity search - Component
Biological speciesENDOTHIA PARASITICA (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1 Å
AuthorsCoates, L. / Erskine, P.T. / Crump, M.P. / Wood, S.P. / Cooper, J.B.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Five Atomic Resolution Structures of Endothiapepsin Inhibitor Complexes: Implications for the Aspartic Proteinase Mechanism
Authors: Coates, L. / Erskine, P.T. / Crump, M.P. / Wood, S.P. / Cooper, J.B.
History
DepositionFeb 27, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Derived calculations
Category: struct_conn / struct_ref_seq_dif
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_rmsd_angle / struct_conn / struct_site
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)34,6524
Polymers33,7961
Non-polymers8563
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.881, 75.446, 43.226
Angle α, β, γ (deg.)90.00, 97.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDOTHIAPEPSIN / ASPARTATE PROTEASE


Mass: 33795.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) ENDOTHIA PARASITICA (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Chemical ChemComp-0EM / N-(tert-butoxycarbonyl)-L-phenylalanyl-N-{(1S)-1-[(R)-hydroxy(2-{[(2S)-2-methylbutyl]amino}-2-oxoethyl)phosphoryl]-3-methylbutyl}-3-(1H-imidazol-3-ium-4-yl)-L-alaninamide / PD-130,328


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 663.765 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H52N6O7P
References: N-(tert-butoxycarbonyl)-L-phenylalanyl-N-{(1S)-1-[(R)-hydroxy(2-{[(2S)-2-methylbutyl]amino}-2-oxoethyl)phosphoryl]-3- methylbutyl}-3-(1H-imidazol-3-ium-4-yl)-L-alaninamide
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsASP A54 AND GLY A55 HAVE CYCLISED TO FORM A SUCCINIMIDE, A54.

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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: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growpH: 4.5 / Details: PH 4.50
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 mg/mlenzyme11
2100 mMsodium acetate11

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1→10 Å / Num. obs: 141699 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 3
Reflection shellResolution: 1→1.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 10 Å / % possible obs: 100 % / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.15 8478 5.3 %RANDOM
obs0.128 -100 %-
all-160884 --
Solvent computationSolvent model: MOEWS AND KRETSINGER
Refinement stepCycle: LAST / Resolution: 1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 56 445 2889
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.025
X-RAY DIFFRACTIONs_angle_d0.048
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.111
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.139
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.074
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor obs: 0.128 / Rfactor Rfree: 0.144 / Rfactor Rwork: 0.1207
Solvent computation
*PLUS
Displacement parameters
*PLUS

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