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- PDB-4er1: THE ACTIVE SITE OF ASPARTIC PROTEINASES -

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Basic information

Entry
Database: PDB / ID: 4er1
TitleTHE ACTIVE SITE OF ASPARTIC PROTEINASES
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
PD125967 / Chem-0ZP / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsQuail, J.W. / Cooper, J.B. / Szelke, M. / Blundell, T.L.
Citation
Journal: FEBS Lett. / Year: 1984
Title: The active site of aspartic proteinases
Authors: Pearl, L. / Blundell, T.
#1: Journal: Proc.FEBS Meet. / Year: 1979
Title: Active Site of Acid Proteinases
Authors: Blundell, T.L. / Jones, H.B. / Khan, G. / Taylor, G. / Sewell, T.S. / Pearl, L.H. / Wood, S.P.
#2: Journal: Proc.FEBS Meet. / Year: 1979
Title: The Three-Dimensional Structure of Acid Proteinases
Authors: Blundell, T.L. / Jenkins, J.A. / Khan, G. / Roychowdhury, P. / Sewell, T. / Tickle, I.J. / Wood, E.A.
#3: Journal: Biochim.Biophys.Acta / Year: 1979
Title: Four-Fold Structural Repeat in the Acid Proteases
Authors: Blundell, T.L. / Sewell, B.T. / Mclachlan, A.D.
#4: Journal: Nature / Year: 1978
Title: Structural Evidence for Gene Duplication in the Evolution of Acid Proteases
Authors: Tang, J. / James, M.N.G. / Hsu, I.N. / Jenkins, J.A. / Blundell, T.L.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1977
Title: Homology Among Acid Proteases. Comparison of Crystal Structures at 3 Angstroms Resolution of Acid Proteases from Rhizopus Chinensis and Endothia Parasitica
Authors: Subramanian, E. / Swan, I.D.A. / Liu, M. / Davies, D.R. / Jenkins, J.A. / Tickle, I.J. / Blundell, T.L.
#6: Journal: Adv.Exp.Med.Biol. / Year: 1977
Title: X-Ray Analysis and Circular Dichroism of the Acid Protease from Endothia Parasitica and Chymosin
Authors: Jenkins, J. / Tickle, I. / Sewell, T. / Ungaretti, L. / Wollmer, A. / Blundell, T.
History
DepositionOct 14, 1990Processing site: BNL
Revision 1.0Jan 15, 1991Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: ENDOTHIAPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6292
Polymers33,8141
Non-polymers8151
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.100, 75.800, 43.000
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO E 23 AND PRO E 133 ARE CIS PROLINES.
2: THE INHIBITOR RESIDUE CAL I 3 IS CYCLOHEXYL ALA-LEU WITH THE PEPTIDE BOND REPLACED BY CHOH-CH2.

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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, EC: 3.4.23.6
#2: Chemical ChemComp-0ZP / N-[(1R,2R,4R)-1-(cyclohexylmethyl)-2-hydroxy-6-methyl-4-{[(2R)-2-methylbutyl]carbamoyl}heptyl]-3-(1H-imidazol-3-ium-4-yl)-N~2~-[3-naphthalen-1-yl-2-(naphthalen-1-ylmethyl)propanoyl]-L-alaninamide / PD125967


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 815.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H68N5O4 / References: PD125967
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR SUBCOMPONENT CAL IS CYCLOHEXYL ALA-LEU WITH THE PEPTIDE BOND REPLACED BY CHOH-CH2.
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: 38.88 %
Crystal grow
*PLUS
pH: 6.3 / Method: unknown
Details: referred to 'Jenkins, J. A.', (1975) 'J.Mol.Biol.', 99, 583-590
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium phosphate11dihydrogen, can be replaced with 0.1M sodium acetate
22.7 Mammonium sulphate11
310 %acetone11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 0.16 Å / Lowest resolution: 2.1 Å

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→20 Å / Rfactor Rwork: 0.143
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 / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 60 260 2709
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.025
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d0.05
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor obs: 0.143
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_plane_restr / Dev ideal: 0.018

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