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- PDB-1bxo: ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PH... -

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Basic information

Entry
Database: PDB / ID: 1bxo
TitleACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE INHIBITOR: METHYL CYCLO[(2S)-2-[[(1R)-1-(N-(L-N-(3-METHYLBUTANOYL)VALYL-L-ASPARTYL)AMINO)-3-METHYLBUT YL] HYDROXYPHOSPHINYLOXY]-3-(3-AMINOMETHYL) PHENYLPROPANOATE
ComponentsPROTEIN (PENICILLOPEPSIN)
KeywordsHYDROLASE / PHOSPHONATE INHIBITORS / MACROCYCLE
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-PP7 / Penicillopepsin-1
Similarity search - Component
Biological speciesPenicillium janthinellum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 0.95 Å
AuthorsKhan, A.R. / Parrish, J.C. / Fraser, M.E. / Smith, W.W. / Bartlett, P.A. / James, M.N.G.
Citation
Journal: Biochemistry / Year: 1998
Title: Lowering the entropic barrier for binding conformationally flexible inhibitors to enzymes.
Authors: Khan, A.R. / Parrish, J.C. / Fraser, M.E. / Smith, W.W. / Bartlett, P.A. / James, M.N.
#1: Journal: J.Am.Chem.Soc. / Year: 1998
Title: Macrocyclic Inhibitors of Penicillopepsin. 3. Design, Synthesis, and Evaluation of an Inhibitor Bridged between P2 and P1'
Authors: Smith, W.W. / Bartlett, P.A.
#2: Journal: J.Am.Chem.Soc. / Year: 1998
Title: Macrocyclic Inhibitors of Penicillopepsin. 2.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.
History
DepositionOct 7, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 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 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (PENICILLOPEPSIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7487
Polymers33,4691
Non-polymers1,2796
Water9,512528
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.980, 46.650, 65.710
Angle α, β, γ (deg.)90.00, 115.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-777-

HOH

21A-778-

HOH

31A-966-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein 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

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Non-polymers , 4 types, 532 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PP7 / METHYL CYCLO[(2S)-2-[[(1R)-1-(N-(L-N-(3-METHYLBUTANOYL)VALYL-L-ASPARTYL)AMINO)-3-METHYLBUTYL]HYDROXYPHOSPHINYLOXY]-3-(3-AMINOMETHYL)PHENYLPROPANOATE


Mass: 638.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H47N4O9P
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsMANNOSE 328 C1 ATTACHED TO OG OF SER 3, MANNOSE 329 C1 ATTACHED TO OG1 OF THR 7

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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: 1.91 Å3/Da / Density % sol: 50 %
Crystal growpH: 4.6 / Details: 0.1 M CH3COONA 35% AMMONIUM SULFATE PH 4.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
235 %ammonium sulfate1reservoir
3100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.919
DetectorType: ADSC / Detector: CCD / Date: Nov 15, 1997 / Details: CRYSTAL AND MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 0.95→10 Å / Num. obs: 430728 / % possible obs: 98 % / Redundancy: 2.76 % / Rmerge(I) obs: 0.053 / Rsym value: 0.055 / Net I/σ(I): 3.9
Reflection shellResolution: 0.95→0.98 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 0.036 / % possible all: 53.8
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 156181 / Num. measured all: 430728

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: OTHER
Starting model: 1PPL

1ppl


Resolution: 0.95→10 Å / Num. parameters: 27864 / Num. restraintsaints: 33863 / Cross valid method: UNTIL NEAR END / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1247 43072 10 %10%
all0.1004 430728 --
obs0.0991 -98 %-
Solvent computationSolvent model: BABINET (SWAT)
Refine analyzeNum. disordered residues: 31 / Occupancy sum hydrogen: 2247.6 / Occupancy sum non hydrogen: 2973.4
Refinement stepCycle: LAST / Resolution: 0.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 83 528 2977
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.096
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.123
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.124
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rwork: 0.0991
Solvent computation
*PLUS
Displacement parameters
*PLUS

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