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- PDB-1ppn: STRUCTURE OF MONOCLINIC PAPAIN AT 1.60 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1ppn
TitleSTRUCTURE OF MONOCLINIC PAPAIN AT 1.60 ANGSTROMS RESOLUTION
ComponentsPAPAIN
KeywordsHYDROLASE(SULFHYDRYL PROTEINASE)
Function / homology
Function and homology information


papain / serpin family protein binding / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space
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
METHANOL / Unknown ligand / Papain
Similarity search - Component
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsPickersgill, R.W. / Harris, G.W. / Garman, E.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure of Monoclinic Papain at 1.60 Angstroms Resolution
Authors: Pickersgill, R.W. / Harris, G.W. / Garman, E.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: The Segmented Anisotropic Refinement of Monoclinic Papain by the Application of the Rigid-Body Tls Model and Comparison to Bovine Ribonuclease A
Authors: Harris, G.W. / Pickersgill, R.W. / Howlin, B. / Moss, D.S.
History
DepositionOct 25, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 8, 2015Group: Non-polymer description
Revision 1.4Jun 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
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

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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)23,4843
Polymers23,4521
Non-polymers322
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.700, 50.700, 31.500
Angle α, β, γ (deg.)90.00, 98.40, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: ASP 57 - ARG 58 OMEGA =146.65 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO 152
3: THE SG ATOM OF ACTIVE SITE RESIDUE CYS 25 HAS ANOTHER ATOM BOUND TO IT, TREATED AS AN OXYGEN IN THE REFINEMENT. AN ADDITIONAL OXYGEN ATOM IS PRESENTED AS A HETATM (O) AT THE END OF THE CHAIN.

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Components

#1: Protein PAPAIN


Mass: 23452.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carica papaya (papaya) / References: UniProt: P00784
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal grow
*PLUS
pH: 5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.3 %papain11
225 mM11NaCl
325 %(v/v)methanol11
40.1 Msodium acetate11
567 %(v/v)methanol12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.6 Å / % possible obs: 93 % / Rmerge F obs: 0.0507

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.6→10 Å
Details: A SECOND SITE FOR ASN 169 WAS IDENTIFIED AND REFINED, THE OCCUPANCY OF THE TWO SITES REFINED TO 0.47 AND 0.53. THE SG ATOM OF ACTIVE SITE RESIDUE CYS 25 HAS ANOTHER ATOM BOUND TO IT, TREATED ...Details: A SECOND SITE FOR ASN 169 WAS IDENTIFIED AND REFINED, THE OCCUPANCY OF THE TWO SITES REFINED TO 0.47 AND 0.53. THE SG ATOM OF ACTIVE SITE RESIDUE CYS 25 HAS ANOTHER ATOM BOUND TO IT, TREATED AS AN OXYGEN IN THE REFINEMENT.
RfactorNum. reflection
Rwork0.1596 -
obs-20172
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1655 0 3 226 1884
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.022
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d0.049
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: 'RESTRAINED LEAST-SQUARES' / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 10 Å / Num. reflection obs: 20172 / Rfactor obs: 0.1596
Solvent computation
*PLUS
Displacement parameters
*PLUS

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