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- PDB-1ent: X-RAY ANALYSES OF ASPARTIC PROTEINASES. THE THREE-DIMENSIONAL STR... -

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Entry
Database: PDB / ID: 1ent
TitleX-RAY ANALYSES OF ASPARTIC PROTEINASES. THE THREE-DIMENSIONAL STRUCTURE AT 2.1 ANGSTROMS RESOLUTION OF ENDOTHIAPEPSIN
ComponentsENDOTHIAPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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
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 speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBlundell, T.L. / Dealwis, C.G.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: X-ray analyses of aspartic proteinases. The three-dimensional structure at 2.1 A resolution of endothiapepsin.
Authors: Blundell, T.L. / Jenkins, J.A. / Sewell, B.T. / Pearl, L.H. / Cooper, J.B. / Tickle, I.J. / Veerapandian, B. / Wood, S.P.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: X-Ray Analyses of Aspartic Proteinases. III Three-Dimensional Structure of Endothiapepsin Complexed with a Transition-State Isostere Inhibitor of Renin at 1.6 Angstroms Resolution
Authors: Veerapandian, B. / Cooper, J.B. / Sali, A. / Blundell, T.L.
History
DepositionMar 11, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Oct 30, 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 / _pdbx_entry_details.has_protein_modification / _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
E: ENDOTHIAPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6704
Polymers33,8141
Non-polymers8563
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.000, 75.700, 42.900
Angle α, β, γ (deg.)90.00, 97.10, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO E 23 / 2: CIS PROLINE - PRO E 133

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Components

#1: Protein ENDOTHIAPEPSIN


Mass: 33813.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryphonectria 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.: 264 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PHOSPHINATE INHIBITOR PD130328 COMPLEXED WITH ENDOTHIAPEPSIN HAS TWO SHORT HYDROGEN BONDS OF 2. ...THE PHOSPHINATE INHIBITOR PD130328 COMPLEXED WITH ENDOTHIAPEPSIN HAS TWO SHORT HYDROGEN BONDS OF 2.44 ANGSTROMS AND 2.51 ANGSTROMS BETWEEN ASP 32 AND P-02 OF THE PHOSPHINATE AND BETWEEN ASP 215 AND P-01 OF THE PHOSPHINATE, RESPECTIVELY. SHORT HYDROGEN BONDS OF THE SAME MAGNITUDE HAVE BEEN OBSERVED WITH SEVERAL SMALL MOLECULE STRUCTURES OF PHOSPHOROUS DERIVATIVES (CALLERI AND SPEAKMAN 1964; SPEAKMAN 1972; FENSKE ET AL., 1973).
Has protein modificationY
Sequence detailsTHE COMPLETE SEQUENCE WAS DETERMINED BY V. PEDERSEN AS TRYPTIC FRAGMENTS WHICH WERE ALIGNED IN THE ...THE COMPLETE SEQUENCE WAS DETERMINED BY V. PEDERSEN AS TRYPTIC FRAGMENTS WHICH WERE ALIGNED IN THE ELECTRON DENSITY. HOMOLOGY WITH OTHER ASPARTIC PROTEINASES WAS USED TO RESOLVE ALIGNMENT AMBIGUITIES. THE RESIDUE NUMBERING IS BASED ON THAT OF PORCINE PEPSIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal grow
*PLUS
pH: 4.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mg/mlprotein11
20.1 Msodium acetate11
355 %satammonium sulfate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 19356 / Num. measured all: 44358 / Rmerge(I) obs: 0.074

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementRfactor obs: 0.17 / Highest resolution: 1.9 Å
Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE *ATOM* AND *HETATM* RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE ...Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE *ATOM* AND *HETATM* RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE DERIVED BY THE FOLLOWING RELATION - B = 8 * (PI)**2 * U**2. IT IS AN INDICATION OF POSSIBLE ERRORS IN THE REFINEMENT THAT SOME ARE SLIGHTLY NEGATIVE.
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 56 264 2709
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d0.007
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Rfactor obs: 0.178 / Lowest resolution: 20 Å / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.9 Å2

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