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- PDB-1epm: A STRUCTURAL COMPARISON OF 21 INHIBITOR COMPLEXES OF THE ASPARTIC... -

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Basic information

Entry
Database: PDB / ID: 1epm
TitleA STRUCTURAL COMPARISON OF 21 INHIBITOR COMPLEXES OF THE ASPARTIC PROTEINASE FROM ENDOTHIA PARASITICA
Components
  • ENDOTHIAPEPSIN
  • PS2, THR-PHE-GLN-ALA-PSA-LEU-ARG-GLU
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
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsCrawford, M. / Cooper, J.B. / Strop, P. / Blundell, T.L.
Citation
Journal: Protein Sci. / Year: 1994
Title: A structural comparison of 21 inhibitor complexes of the aspartic proteinase from Endothia parasitica.
Authors: Bailey, D. / Cooper, J.B.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: The 3D Structure at 2 Angstroms Resolution of Endothiapepsin
Authors: Blundell, T.L. / Jenkins, J. / Sewell, B.T. / Pearl, L.H. / Cooper, J.B. / Tickle, I.J. / Veerapandian, B. / Wood, S.P.
History
DepositionJul 27, 1994Processing site: BNL
Revision 1.0Dec 20, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 10, 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 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 6, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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
I: PS2, THR-PHE-GLN-ALA-PSA-LEU-ARG-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1585
Polymers34,8702
Non-polymers2883
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-39 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.110, 75.880, 42.980
Angle α, β, γ (deg.)90.00, 96.76, 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: Protein/peptide PS2, THR-PHE-GLN-ALA-PSA-LEU-ARG-GLU


Mass: 1056.192 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsRESIDUE I 5 IS A STANDARD THR. RESIDUE I 4 IS A STANDARD PHE. RESIDUE I 3 IS A STANDARD GLN. ...RESIDUE I 5 IS A STANDARD THR. RESIDUE I 4 IS A STANDARD PHE. RESIDUE I 3 IS A STANDARD GLN. RESIDUE I 2 IS A STANDARD ALA. RESIDUE I 1 (PSA) IS A PHENYLSTATINE (I.E. IT HAS A PHE SIDE CHAIN BUT HAS A -CHOH-CH(2)-CO- INSTEAD OF MAIN CHAIN -CO- GROUP. RESIDUE I 2' IS A STANDARD LEU. RESIDUE I 3' IS A STANDARD ARG. RESIDUE I 4' IS A STANDARD GLU.
Sequence detailsRESIDUES 63A, 80A, 134A, 184A, 203A, 204A, 238A, 282A, 282B, AND 319A IN CHAIN E ARE INSERTIONS ...RESIDUES 63A, 80A, 134A, 184A, 203A, 204A, 238A, 282A, 282B, AND 319A IN CHAIN E ARE INSERTIONS RELATIVE TO 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 Å3/Da / Density % sol: 38.54 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementResolution: 1.6→20 Å / Rfactor obs: 0.17
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 15 281 2759
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS

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