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- PDB-1ppm: CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PEN... -

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Basic information

Entry
Database: PDB / ID: 1ppm
TitleCRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES
ComponentsPENICILLOPEPSIN
KeywordsHYDROLASE/hydrolase inhibitor / ACID PROTEINASE / HYDROLASE-hydrolase inhibitor complex
Function / homology
Function and homology information


penicillopepsin / aspartic-type endopeptidase activity / proteolysis / extracellular region
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
Cbz-Ala-Ala-Leu(P)-(O)-Phe-OMe / Chem-0P1 / alpha-L-arabinopyranose / alpha-D-mannopyranose / Penicillopepsin-1
Similarity search - Component
Biological speciesPenicillium janthinellum (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsFraser, M.E. / James, M.N.G.
Citation
Journal: Biochemistry / Year: 1992
Title: Crystallographic analysis of transition-state mimics bound to penicillopepsin: phosphorus-containing peptide analogues.
Authors: Fraser, M.E. / Strynadka, N.C. / Bartlett, P.A. / Hanson, J.E. / James, M.N.
#1: Journal: Biological Macromolecules and Assemblies / Year: 1987
Title: Aspartic Proteinases and Their Catalytic Pathway
Authors: James, M.N.G. / Sielecki, A.R.
#2: Journal: Biochemistry / Year: 1985
Title: Stereochemical Analysis of Peptide Bond Hydrolysis Catalyzed by the Aspartic Proteinase Penicillopepsin
Authors: James, M.N.G. / Sielecki, A.R.
#3: Journal: J.Mol.Biol. / Year: 1983
Title: Structure and Refinement of Penicillopepsin at 1.8 Angstroms Resolution
Authors: James, M.N.G. / Sielecki, A.R.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Conformational Flexibility in the Active Sites of Aspartyl Proteinases Revealed by a Pepstatin Fragment Binding to Penicillopepsin
Authors: James, M.N.G. / Sielecki, A. / Salituro, F. / Rich, D.H. / Hofmann, T.
#5: Journal: STRUCTURAL STUDIES ON MOLECULES OF BIOLOGICA INTERESTL
Year: 1981
Title: The Tertiary Structure of Penicillopepsin. Towards a Catalytic Mechanism for Acid Proteases
Authors: James, M.N.G. / Hsu, I-N. / Hofmann, T. / Sielecki, A.R.
#6: Journal: Can.J.Biochem. / Year: 1980
Title: An X-Ray Crystallographic Approach to Enzyme Structure and Function
Authors: James, M.N.G.
#7: Journal: Nature / Year: 1978
Title: Structural Evidence for Gene Duplication in the Evolution of the Acid Proteases
Authors: Tang, J. / James, M.N.G. / Hsu, I.N. / Jenkins, J.A. / Blundell, T.L.
#8: Journal: Nature / Year: 1977
Title: Mechanism of Acid Protease Catalysis Based on the Crystal Structure of Penicillopepsin
Authors: James, M.N.G. / Hsu, I.-N. / Delbaere, L.T.J.
#9: Journal: Nature / Year: 1977
Title: Penicillopepsin from Penicillium Janthinellum Crystal Structure at 2.8 Angstroms and Sequence Homology with Porcine Pepsin
Authors: Hsu, I.-N. / Delbaere, L.T.J. / James, M.N.G. / Hofmann, T.
#10: Journal: Adv.Exp.Med.Biol. / Year: 1977
Title: Penicillopepsin. 2.8 Angstroms Structure, Active Site Conformation and Mechanistic Implications
Authors: Hsu, I-N. / Delbaere, L.T.J. / James, M.N.G. / Hofmann, T.
#11: Journal: Biochem.Biophys.Res.Commun. / Year: 1976
Title: The Crystal Structure of Penicillopepsin at 6 Angstroms Resolution
Authors: Hsu, I-N. / Hofmann, T. / Nyburg, S.C. / James, M.N.G.
History
DepositionJun 1, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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 1.4Jul 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_status / software / struct_conn
Item: _pdbx_database_status.process_site / _software.classification / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: PENICILLOPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5015
Polymers33,4691
Non-polymers1,0324
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.400, 46.590, 66.290
Angle α, β, γ (deg.)90.00, 115.70, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUES 134 AND 315 ARE CIS PROLINES.
Components on special symmetry positions
IDModelComponents
11E-374-

HOH

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Components

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Protein , 1 types, 1 molecules E

#1: Protein PENICILLOPEPSIN


Mass: 33468.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium janthinellum (fungus) / References: UniProt: P00798, penicillopepsin

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Sugars , 2 types, 2 molecules

#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-ARA / alpha-L-arabinopyranose / alpha-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinopyranoseCOMMON NAMEGMML 1.0
a-L-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 308 molecules

#2: Chemical ChemComp-0P1 / N-[(benzyloxy)carbonyl]-L-alanyl-N-{(1S)-1-[(R)-[(1R)-1-benzyl-2-methoxy-2-oxoethoxy](hydroxy)phosphoryl]-3-methylbutyl }-L-alaninamide / Cbz-Ala-Ala-Leu(P)-(O)-Phe-OMe


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 605.616 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H40N3O9P / References: Cbz-Ala-Ala-Leu(P)-(O)-Phe-OMe
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsXYS IS POORLY DEFINED IN THE ELECTRON DENSITY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.19 %
Crystal grow
*PLUS
Temperature: 18-22 ℃ / pH: 4.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlcomplex1drop
234-40 %satammonium sulfate1drop
30.1 M1dropNaC2H3O2

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 60 Å / Num. all: 29687 / Num. obs: 26564 / Num. measured all: 100309 / Rmerge(I) obs: 0.055

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.15 / Rfactor obs: 0.15 / Highest resolution: 1.7 Å
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 67 306 2739
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 8 Å / Num. reflection obs: 25614 / Rfactor obs: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d0.043
X-RAY DIFFRACTIONx_planar_d0.045
X-RAY DIFFRACTIONx_plane_restr0.019
X-RAY DIFFRACTIONx_chiral_restr0.163

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