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- PDB-1bp4: USE OF PAPAIN AS A MODEL FOR THE STRUCTURE-BASED DESIGN OF CATHEP... -

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Basic information

Entry
Database: PDB / ID: 1bp4
TitleUSE OF PAPAIN AS A MODEL FOR THE STRUCTURE-BASED DESIGN OF CATHEPSIN K INHIBITORS. CRYSTAL STRUCTURES OF TWO PAPAIN INHIBITOR COMPLEXES DEMONSTRATE BINDING TO S'-SUBSITES.
ComponentsPAPAIN
KeywordsHYDROLASE / SULFHYDRYL PROTEINASE
Function / homology
Function and homology information


papain / serpin family protein binding / cysteine-type peptidase activity / proteolysis
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHQ-Leu-Leu-Leu-aldehyde MG-132, bound form / Chem-ALD / Papain
Similarity search - Component
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLalonde, J.M. / Zhao, B. / Smith, W.W. / Janson, C.A. / Desjarlais, R.L. / Tomaszek, T.A. / Carr, T.J. / Thompson, S.K. / Yamashita, D.S. / Veber, D.F. / Abdel-Mequid, S.S.
CitationJournal: J.Med.Chem. / Year: 1998
Title: Use of papain as a model for the structure-based design of cathepsin K inhibitors: crystal structures of two papain-inhibitor complexes demonstrate binding to S'-subsites.
Authors: LaLonde, J.M. / Zhao, B. / Smith, W.W. / Janson, C.A. / DesJarlais, R.L. / Tomaszek, T.A. / Carr, T.J. / Thompson, S.K. / Oh, H.J. / Yamashita, D.S. / Veber, D.F. / Abdel-Meguid, S.S.
History
DepositionAug 12, 1998Processing site: BNL
Revision 1.0Aug 12, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2012Group: Non-polymer description
Revision 1.4Nov 9, 2016Group: Non-polymer description
Revision 1.5Mar 7, 2018Group: Advisory / Data collection / Other
Category: diffrn_source / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.6Aug 9, 2023Group: Advisory / Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.7Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PAPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9272
Polymers23,4491
Non-polymers4781
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.540, 50.740, 62.280
Angle α, β, γ (deg.)90.00, 99.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PAPAIN


Mass: 23449.346 Da / Num. of mol.: 1 / Fragment: NON / Source method: isolated from a natural source
Details: ALDEHYDE INHIBITOR COVALENTLY BOUND TO ACTIVE SITE CYS 25 AS A HEMIMERCAPTAL. BOND OCCURS BETWEEN CYS 25-SG AND ALD 213-C22
Source: (natural) Carica papaya (papaya) / References: UniProt: P00784
#2: Chemical ChemComp-ALD / N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide


Type: Peptide-like / Class: Inhibitor / Mass: 477.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H43N3O5 / References: PHQ-Leu-Leu-Leu-aldehyde MG-132, bound form
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 6

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-HCl1reservoir
20.5 Mtrisodium citrate1reservoir
320 %PEG6001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1995
RadiationMonochromator: MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→10 Å / Num. obs: 14458 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.104 / Rsym value: 0.088 / Net I/σ(I): 7.9
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.27 / % possible all: 60
Reflection
*PLUS
Num. measured all: 62560 / Rmerge(I) obs: 0.0878

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PIP

1pip


Resolution: 2.2→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
Details: DISORDERED SIDE-CHAINS HAVE OCCUPANCIES SET TO ZERO IN COORDINATE FILE, RESIDUES 59,73,78,84,93,94,98,111,114,129,145
RfactorNum. reflection% reflectionSelection details
Rfree0.24 727 8.2 %RANDOM
Rwork0.19 ---
obs0.19 12955 81 %-
Displacement parametersBiso mean: 22.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1655 0 34 88 1777
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.529
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.74
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.387
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
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.279 58 3 %
Rwork0.269 654 -
obs--28 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.743
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.387

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