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- PDB-2wed: ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PH... -

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Basic information

Entry
Database: PDB / ID: 2wed
TitleACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE MACROCYCLIC INHIBITOR:METHYL[CYCLO-7[(2R)-((N-VALYL)AMINO)-2-(HYDROXYL-(1S)-1-METHYOXYCARBONYL-2-PHENYLETHOXY)PHOSPHINYLOXY-ETHYL]-1-NAPHTHALENEACETAMIDE], SODIUM SALT
ComponentsPENICILLOPEPSIN
KeywordsHYDROLASE / PENICILLOPEPSIN / MACROCYCLIC INHIBITOR
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
alpha-D-mannopyranose / Chem-PP6 / Penicillopepsin-1
Similarity search - Component
Biological speciesPenicillium janthinellum (fungus)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER METHOD / Resolution: 1.5 Å
AuthorsDing, J. / Fraser, M.E. / James, M.N.G.
Citation
Journal: J.Am.Chem.Soc. / Year: 1998
Title: Macrocyclic Inhibitors of Penicillopepsin. II. X-Ray Crystallographic Analyses of Penicillopepsin Complexed with a P3-P1 Macrocyclic Peptidyl Inhibitor and with its Two Acyclic Analogues
Authors: Ding, J. / Fraser, M.E. / Meyer, J.H. / Bartlett, P.A. / James, M.N.G.
#1: Journal: To be Published
Title: Macrocyclic Inhibitors of Penicillopepsin. I. Design, Synthesis, and Evaluation of an Inhibitor Bridged between P1 and P3
Authors: Meyer, J.H. / Bartlett, P.A.
#2: 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.
#3: 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.
History
DepositionFeb 3, 1998Processing site: BNL
SupersessionMay 27, 1998ID: 1WED
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jul 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_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 23, 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 / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PENICILLOPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4775
Polymers33,4691
Non-polymers1,0084
Water5,062281
1
A: PENICILLOPEPSIN
hetero molecules

A: PENICILLOPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,95310
Polymers66,9382
Non-polymers2,0168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)97.880, 46.640, 66.590
Angle α, β, γ (deg.)90.00, 116.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-524-

HOH

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Components

#1: Protein PENICILLOPEPSIN


Mass: 33468.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Penicillium janthinellum (fungus) / References: UniProt: P00798, penicillopepsin
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PP6 / METHYL[CYCLO-7[(2R)-((N-VALYL)AMINO)-2-(HYDROXYL-(1S)-1-METHYLOXYCARBONYL-2-PHENYLETHOXY)PHOSPHINYLOXY-ETHYL]-1-NAPHTHALENEACETAMIDE]


Mass: 551.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H32N2O7P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growpH: 4.4 / Details: 0.1M NAC2H3O2 PH=4.4 35-40% SATURATED (NH4)2SO4

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 16, 1997 / Details: DOUBLE-MIRRORS FOCUSING
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 38650 / % possible obs: 89.18 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 13.64 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.98
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 3.4 / % possible all: 77.55

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
TNT5Erefinement
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER METHOD / Resolution: 1.5→20 Å / σ(F): 2
Details: X-PLOR, TNT ESD FROM SIGMAA (A) : 0.149658 UNCERTAINTY IN RMS ERROR SQUARED : 0.002037
RfactorNum. reflection% reflection
Rfree0.19 -10 %
Rwork0.154 --
obs0.158 36649 84 %
all-38650 -
Solvent computationBsol: 118.5 Å2 / ksol: 0.631 e/Å3
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 72 281 2728
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0125071
X-RAY DIFFRACTIONt_angle_deg1.30534001
X-RAY DIFFRACTIONt_dihedral_angle_d14.98814075
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.012682
X-RAY DIFFRACTIONt_gen_planes0.0193673
X-RAY DIFFRACTIONt_it1.45625070.55
X-RAY DIFFRACTIONt_nbd0.019379

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