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- PDB-1eed: X-ray crystallographic analysis of inhibition of endothiapepsin b... -

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Basic information

Entry
Database: PDB / ID: 1eed
TitleX-ray crystallographic analysis of inhibition of endothiapepsin by cyclohexyl renin inhibitors
ComponentsENDOTHIAPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ASPARTIC 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
(6R,7S,12R,13R,17R)-6-benzyl-12-(cyclohexylmethyl)-7,13-dihydroxy-2,2-dimethyl-17-(2-methylpropyl)- 4,10,15-trioxo-3-oxa-5,11,16-triazaoctadecan-18-oic acid / Chem-0EO / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBlundell, T.L. / Frazao, C. / Cooper, J.B.
CitationJournal: Biochemistry / Year: 1992
Title: X-ray crystallographic analysis of inhibition of endothiapepsin by cyclohexyl renin inhibitors.
Authors: Cooper, J. / Quail, W. / Frazao, C. / Foundling, S.I. / Blundell, T.L. / Humblet, C. / Lunney, E.A. / Lowther, W.T. / Dunn, B.M.
History
DepositionJun 15, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: ENDOTHIAPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4482
Polymers33,8141
Non-polymers6341
Water5,008278
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, 75.700, 42.900
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 23 / 2: CIS PROLINE - PRO 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-0EO / (2S)-2-[[(3S,4S)-5-cyclohexyl-4-[[(4S,5S)-5-[(2-methylpropan-2-yl)oxycarbonylamino]-4-oxidanyl-6-phenyl-hexanoyl]amino]-3-oxidanyl-pentanoyl]amino]-4-methyl-pentanoic acid / PD125754


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 633.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H55N3O8
References: (6R,7S,12R,13R,17R)-6-benzyl-12-(cyclohexylmethyl)-7,13-dihydroxy-2,2-dimethyl-17-(2-methylpropyl)- 4,10,15-trioxo-3-oxa-5,11,16-triazaoctadecan-18-oic acid
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR PD125754 EXTENDS FROM P4 TO P2'. THE INHIBITOR HAS A TERT-BUTYL OXY CARBONYL (BOG) AT ...THE INHIBITOR PD125754 EXTENDS FROM P4 TO P2'. THE INHIBITOR HAS A TERT-BUTYL OXY CARBONYL (BOG) AT P4, A PHE-GLY DIPEPTIDE HYDROXYETHYLENE ANALOGUE (FOG)AT P3-P2, A CYCLOHEXYL STATINE (CHS) AT P1-P1', A LEUCINE AT P2' AND A DIAMINOMETHYLBENZENE AT P3' WHICH COULD NOT BE LOCATED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.05 %
Crystal grow
*PLUS
Method: unknown / Details: Moews, P., (1970) J. Mol. Biol., 54, 395. / PH range low: 6.3 / PH range high: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.2 Mammonium sulfate11
30.1 Msodium dihydrogen11
2acetate11can be replaced with phosphate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 18024 / % possible obs: 99 % / Num. measured all: 88024 / Rmerge(I) obs: 0.095

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementRfactor Rwork: 0.152 / Highest resolution: 2 Å
Details: THE ATOMIC TEMPERATURE FACTORS IN THIS ENTRY ARE GIVEN AS U VALUES NOT B VALUES. B VALUES MAY BE CALCULATED BY THE THE FOLLOWING: BISO (BISO = 8 PI==2== UISO).
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 45 278 2712
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.024
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d0.029
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
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor obs: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS

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