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- PDB-1pe6: REFINED X-RAY STRUCTURE OF PAPAIN(DOT)E-64-C COMPLEX AT 2.1-ANGST... -

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Basic information

Entry
Database: PDB / ID: 1pe6
TitleREFINED X-RAY STRUCTURE OF PAPAIN(DOT)E-64-C COMPLEX AT 2.1-ANGSTROMS RESOLUTION
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
Chem-E6C / METHANOL / Papain
Similarity search - Component
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsYamamoto, D. / Matsumoto, K. / Ohishi, H. / Ishida, T. / Inoue, M. / Kitamura, K. / Mizuno, H.
Citation
Journal: J.Biol.Chem. / Year: 1991
Title: Refined x-ray structure of papain.E-64-c complex at 2.1-A resolution.
Authors: Yamamoto, D. / Matsumoto, K. / Ohishi, H. / Ishida, T. / Inoue, M. / Kitamura, K. / Mizuno, H.
#1: Journal: FEBS Lett. / Year: 1989
Title: Mode of Binding of E-64-C, a Potent Thiol Protease Inhibitor, to Papain as Determined by X-Ray Crystal Analysis of the Complex
Authors: Matsumoto, K. / Yamamoto, D. / Ohishi, H. / Tomoo, K. / Ishida, T. / Inoue, M. / Sadatome, T. / Kitamura, K. / Mizuno, H.
#2: Journal: FEBS Lett. / Year: 1990
Title: The Importance of Val-157 Hydrophobic Interaction for Papain Inhibitory Activity of an Epoxysuccinyl Amino Acid Derivative; a Structure-Activity Relationship Based on the Crystal Structure of ...Title: The Importance of Val-157 Hydrophobic Interaction for Papain Inhibitory Activity of an Epoxysuccinyl Amino Acid Derivative; a Structure-Activity Relationship Based on the Crystal Structure of the Papain-E-64-C Complex
Authors: Yamamoto, D. / Matsumoto, K. / Ohishi, H. / Ishida, T. / Inoue, M. / Kitamura, K. / Mizuno, H.
History
DepositionMay 14, 1991Processing site: BNL
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 4, 5, 6 OF S1A ARE IDENTICAL TO STRANDS 2, 3, 4 OF SHEET S1B.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PAPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,21416
Polymers23,4491
Non-polymers76515
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.900, 95.510, 49.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE PRO 152 IS A CIS PROLINE. / 2: SEE REMARK 6.

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Components

#1: Protein PAPAIN /


Mass: 23449.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carica papaya (papaya) / References: UniProt: P00784, papain
#2: Chemical ChemComp-E6C / N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE


Mass: 316.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28N2O5
#3: Chemical
ChemComp-MOH / METHANOL / Methanol


Mass: 32.042 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: CH4O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SG ATOM OF CYS 25, THE CATALYTIC CENTER OF PAPAIN, COVALENTLY BONDS TO THE C2 ATOM OF E-64-C, ...THE SG ATOM OF CYS 25, THE CATALYTIC CENTER OF PAPAIN, COVALENTLY BONDS TO THE C2 ATOM OF E-64-C, AND THE LEUCYL AND ISOAMYLAMIDE GROUPS OF E-64-C INTERACT WITH THE RESIDUES OF PAPAIN S SUBSITES. NOTE ESPECIALLY THAT A HYDROGEN BONDING PAIR, FASHIONED LIKE A PARALLEL BETA-SHEET, IS FORMED BETWEEN THE PEPTIDE MOIETIES OF E-64-C AND RESIDUE GLY 66. THE CRYSTALS USED IN THIS STUDY ARE OF THE D TYPE.
Nonpolymer detailsE6C IS (2S,3S)-3-(1-(N-(3-METHYLBUTYL)AMINO)- LEUCYLCARBOXYL)OXIRANE-2-CARBOXYLATE. THIS COMPOUND ...E6C IS (2S,3S)-3-(1-(N-(3-METHYLBUTYL)AMINO)- LEUCYLCARBOXYL)OXIRANE-2-CARBOXYLATE. THIS COMPOUND WAS DESIGNED FROM THE NATURAL PRODUCT E-64. E-64-C CONSISTS OF L-TRANSEPOXYSUCCINYL, L-LEUCYL, AND ISOAMYLAMIDE MOIETIES, AND THE CARBON ATOMS OF THE EPOXY RING HAVE AN R CONFIGURATION IN THIS COMPLEX. NOTE THAT THE BOND BETWEEN ATOMS O1 AND C2 IS BROKEN WHEN E-64-C BINDS TO PAPAIN IN THIS STRUCTURE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.5 %(w/v)enzyme1drop
27.6 mM1dropNaCl
342.6 %(w/v)methanol1drop
421.3 %(w/v)ethanol1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 12794 / Rmerge(I) obs: 0.027 / Biso Wilson estimate: 11.1 Å2

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.1→6 Å /
RfactorNum. reflection
obs0.159 10168
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1655 0 50 181 1886
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.040.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0450.045
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.751
X-RAY DIFFRACTIONp_mcangle_it1.2511.5
X-RAY DIFFRACTIONp_scbond_it0.8451
X-RAY DIFFRACTIONp_scangle_it1.4821.5
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1590.14
X-RAY DIFFRACTIONp_singtor_nbd0.1860.25
X-RAY DIFFRACTIONp_multtor_nbd0.1720.25
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2430.25
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.43
X-RAY DIFFRACTIONp_staggered_tor1825
X-RAY DIFFRACTIONp_orthonormal_tor2930
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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