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- PDB-3er5: THE ACTIVE SITE OF ASPARTIC PROTEINASES -

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Basic information

Entry
Database: PDB / ID: 3er5
TitleTHE ACTIVE SITE OF ASPARTIC PROTEINASES
Components
  • ENDOTHIAPEPSIN
  • H-189
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Peptide ligand-binding receptors / Metabolism of Angiotensinogen to Angiotensins / : / type 2 angiotensin receptor binding / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / acrosome reaction / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of macrophage derived foam cell differentiation / positive regulation of extracellular matrix assembly ...Peptide ligand-binding receptors / Metabolism of Angiotensinogen to Angiotensins / : / type 2 angiotensin receptor binding / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / acrosome reaction / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of macrophage derived foam cell differentiation / positive regulation of extracellular matrix assembly / calcium-ion regulated exocytosis / vasoconstriction / type 1 angiotensin receptor binding / positive regulation of extrinsic apoptotic signaling pathway / G alpha (q) signalling events / positive regulation of epidermal growth factor receptor signaling pathway / G alpha (i) signalling events / positive regulation of gap junction assembly / regulation of cardiac conduction / endothiapepsin / positive regulation of epithelial to mesenchymal transition / positive regulation of protein metabolic process / positive regulation of endothelial cell migration / kidney development / angiotensin-activated signaling pathway / serine-type endopeptidase inhibitor activity / hormone activity / positive regulation of miRNA transcription / regulation of apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / aspartic-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
Angiotensinogen / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors ...Angiotensinogen / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / 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
H 189 / Angiotensinogen / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsBailey, D. / Veerapandian, B. / Cooper, J. / Szelke, M. / Blundell, T.L.
Citation
Journal: Biochem.J. / Year: 1993
Title: X-ray-crystallographic studies of complexes of pepstatin A and a statine-containing human renin inhibitor with endothiapepsin.
Authors: Bailey, D. / Cooper, J.B. / Veerapandian, B. / Blundell, T.L. / Atrash, B. / Jones, D.M. / Szelke, M.
#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
DepositionJan 5, 1991Processing site: BNL
Revision 1.0Apr 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

Downloads & links

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Assembly

Deposited unit
E: ENDOTHIAPEPSIN
I: H-189


Theoretical massNumber of molelcules
Total (without water)35,0862
Polymers35,0862
Non-polymers00
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-12 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.100, 75.400, 42.800
Angle α, β, γ (deg.)90.00, 97.00, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUE PRO E 23 AND PRO E 133 ARE CIS PROLINES.

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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: Protein/peptide H-189


Type: Peptide-like / Class: Inhibitor / Mass: 1272.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P01017, H 189
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
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: 1.97 Å3/Da / Density % sol: 37.45 %
Crystal grow
*PLUS
pH: 4.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160 mMprotein11
20.1 Macetate11
3600 mMpepstatin11
42.2 Mammonium sulfate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 23224 / Num. measured all: 36927 / Rmerge F obs: 0.039

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→10 Å / Rfactor Rwork: 0.15
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: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 0 223 2703
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.02
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d0.04
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: 1.8 Å / Lowest resolution: 10 Å / Num. reflection obs: 21972 / σ(F): 2 / Rfactor obs: 0.152 / Rfactor Rwork: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_plane_restr / Dev ideal: 0.013

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