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

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Basic information

Entry
Database: PDB / ID: 1apw
TitleCRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: DIFLUOROSTATINE-AND DIFLUOROSTATONE-CONTAINING PEPTIDES
Components
  • INHIBITOR ISOVALERYL (IVA)-VAL-VAL-DIFLUOROSTATINE-N-METHYLAMINE
  • PENICILLOPEPSIN
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
DIMETHYLFORMAMIDE / alpha-L-xylopyranose / alpha-D-mannopyranose / Penicillopepsin-1
Similarity search - Component
Biological speciesPenicillium janthinellum (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSielecki, A.R. / James, M.N.G.
Citation
Journal: Biochemistry / Year: 1992
Title: Crystallographic analysis of transition state mimics bound to penicillopepsin: difluorostatine- and difluorostatone-containing peptides.
Authors: James, M.N. / Sielecki, A.R. / Hayakawa, K. / Gelb, M.H.
#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: Aspartic Proteinases and Their Inhibitors / Year: 1985
Title: X-Ray Diffraction Studies on Penicillopepsin and its Complexes: The Hydrolytic Mechanism
Authors: James, M.N.G. / Sielecki, A.R. / Hofmann, T.
#4: Journal: Biochemistry / Year: 1984
Title: Effect of Ph on the Activities of Penicillopepsin and Rhizopus Pepsin and a Proposal for the Productive Substrate Binding Mode in Penicillopepsin
Authors: Hofmann, T. / Hodges, R.S. / James, M.N.G.
#5: Journal: Peptides: Structure and Function, Proceedings of the of the Eighth American Peptide Symposium
Year: 1983
Title: Crystallographic Analysis of a Pepstatin Analogue Binding to the Aspartyl Proteinase Penicillopepsin at 1.8 Angstroms Resolution
Authors: James, M.N.G. / Sielecki, A.R. / Moult, J.
#6: 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.
#7: 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.
History
DepositionDec 16, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_chiral.auth_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: PENICILLOPEPSIN
I: INHIBITOR ISOVALERYL (IVA)-VAL-VAL-DIFLUOROSTATINE-N-METHYLAMINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4756
Polymers33,9752
Non-polymers4994
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-13 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.640, 46.580, 66.440
Angle α, β, γ (deg.)90.00, 116.12, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUES PRO E 134 AND PRO E 315 ARE CIS PROLINES.
2: THE REGION FROM SER E 277 TO SER E 281 IS POORLY ORDERED.
3: THE FOLLOWING WATER MOLECULES ARE SITTING ON A SPECIAL POSITION: HOH 563, HOH 584 AND HOH 585.
Components on special symmetry positions
IDModelComponents
11E-563-

HOH

21E-584-

HOH

31E-585-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules EI

#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
#2: Protein/peptide INHIBITOR ISOVALERYL (IVA)-VAL-VAL-DIFLUOROSTATINE-N-METHYLAMINE


Mass: 506.626 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TRANSITION STATE MIMIC

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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-HSY / alpha-L-xylopyranose / alpha-L-xylose / L-xylose / xylose


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

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Non-polymers , 3 types, 297 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 38.37 %
Crystal grow
*PLUS
Method: other / Details: NMR

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 45 Å / Num. all: 27895 / Num. obs: 24987 / Rmerge(I) obs: 0.031

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→8 Å / σ(I): 1 /
RfactorNum. reflection
obs0.131 22464
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2401 0 30 295 2726
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 22464 / σ(I): 1 / Rfactor obs: 0.131
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 12.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.043
X-RAY DIFFRACTIONp_planar_d0.044
X-RAY DIFFRACTIONp_plane_restr0.008
X-RAY DIFFRACTIONp_chiral_restr0.195

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