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

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Entry
Database: PDB / ID: 1ppk
TitleCRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHOROUS-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
isovaleryl (IVA)-VAL-VAL-STA(P)-O-ET phosphinic acid analogue of statin / DIMETHYLFORMAMIDE / alpha-L-xylopyranose / Chem-IVV / alpha-D-mannopyranose / Penicillopepsin-1
Similarity search - Component
Biological speciesPenicillium janthinellum (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsStrynadka, N.C.J. / 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: Biochemistry / Year: 1992
Title: Crystallographic Analysis of Transition State Mimics Bound to Penicillopepsin: Difluorostatine-and Difluorostatone-Containing Peptides
Authors: James, M.N.G. / Sielecki, A.R. / Hayakawa, K. / Gelb, M.H.
#2: Journal: Biological Macromolecules and Assemblies / Year: 1987
Title: Aspartic Proteinases and Their Catalytic Pathway
Authors: James, M.N.G. / Sielecki, A.R.
#3: 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.
#4: 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.
#5: 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.
#6: 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.
#7: 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.
#8: 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
DepositionJan 20, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)34,4886
Polymers33,4691
Non-polymers1,0195
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.480, 46.550, 66.420
Angle α, β, γ (deg.)90.00, 116.14, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO E 134 / 2: THE REGION FROM SER E 277 - SER E 281 IS POORLY ORDERED. / 3: CIS PROLINE - PRO E 315
Components on special symmetry positions
IDModelComponents
11E-614-

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 / 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 / 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 , 4 types, 278 molecules

#2: Chemical ChemComp-IVV / N-(3-methylbutanoyl)-L-valyl-N-{(1R)-1-[(R)-(2-ethoxy-2-oxoethyl)(hydroxy)phosphoryl]-3-methylbutyl}-L-valinamide / PHOSPHINIC ACID ANALOGUE OF STATIN (IVA)-VAL-VAL-STA(P)-O-ET


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 519.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46N3O7P
References: isovaleryl (IVA)-VAL-VAL-STA(P)-O-ET phosphinic acid analogue of statin
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


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


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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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: 38.2 %
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
ReflectionHighest resolution: 1.8 Å
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 45 Å / Num. obs: 24917 / Num. measured all: 29429 / Rmerge(I) obs: 0.033

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→8 Å / σ(F): 3 /
RfactorNum. reflection
obs0.132 22145
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 65 275 2706
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.018
X-RAY DIFFRACTIONp_angle_d0.0440.032
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.032
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.91.5
X-RAY DIFFRACTIONp_mcangle_it2.82.5
X-RAY DIFFRACTIONp_scbond_it3.42
X-RAY DIFFRACTIONp_scangle_it53.2
X-RAY DIFFRACTIONp_plane_restr0.0180.018
X-RAY DIFFRACTIONp_chiral_restr0.2130.18
X-RAY DIFFRACTIONp_singtor_nbd0.250.36
X-RAY DIFFRACTIONp_multtor_nbd0.1820.36
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2040.36
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
Rfactor obs: 0.132
Solvent computation
*PLUS
Displacement parameters
*PLUS

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