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- PDB-9pap: STRUCTURE OF PAPAIN REFINED AT 1.65 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 9pap
TitleSTRUCTURE OF PAPAIN REFINED AT 1.65 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
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsKamphuis, I.G. / Drenth, J.
Citation
Journal: J.Mol.Biol. / Year: 1984
Title: Structure of papain refined at 1.65 A resolution
Authors: Kamphuis, I.G. / Kalk, K.H. / Swarte, M.B. / Drenth, J.
#1: Journal: J.Mol.Biol. / Year: 1985
Title: Thiol Proteases. Comparative Studies Based on the High-Resolution Structures of Papain and Actinidin, and on Amino Acid Sequence Information for Cathepsins B and H, and Stem Bromelain
Authors: Kamphuis, I.G. / Drenth, J. / Baker, E.N.
#2: Journal: Biochemistry / Year: 1976
Title: Binding of Chloromethyl Ketone Substrate Analogues to Crystalline Papain
Authors: Drenth, J. / Kalk, K.H. / Swen, H.M.
#3: Journal: Adv.Protein Chem. / Year: 1971
Title: The Structure of Papain
Authors: Drenth, J. / Jansonius, J.N. / Koekoek, R. / Wolthers, B.G.
#4: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1970
Title: The Structure of the Papain Molecule
Authors: Drenth, J. / Jansonius, J.N. / Koekoek, R. / Sluyterman, L.A.A. / Wolthers, B.G.
#5: Journal: Nature / Year: 1968
Title: Structure of Papain
Authors: Drenth, J. / Jansonius, J.N. / Koekoek, R. / Swen, H.M. / Wolthers, B.G.
History
DepositionMar 31, 1986Processing site: BNL
SupersessionOct 24, 1986ID: 3PAD, 8PAP
Revision 1.0Oct 24, 1986Provider: repository / Type: Initial release
SupersessionJan 15, 1987ID: 8PAP
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_PDB_obs_spr / pdbx_database_status ...pdbx_database_PDB_obs_spr / pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_PDB_obs_spr.replace_pdb_id / _pdbx_database_status.process_site

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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)24,42730
Polymers23,4971
Non-polymers92929
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.200, 104.640, 50.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE 152 IS A CIS PROLINE. / 2: SEE REMARK 5 ABOVE.

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Components

#1: Protein PAPAIN


Mass: 23497.344 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-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: CH4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein11
267 %(v/v)methanol-water mixture11

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.161 / Highest resolution: 1.65 Å
Refinement stepCycle: LAST / Highest resolution: 1.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1655 0 0 253 1908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d0.047
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection all: 24350 / Rfactor obs: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_planar_d0.044
X-RAY DIFFRACTIONp_chiral_restr0.017
X-RAY DIFFRACTIONp_mcbond_it5.98
X-RAY DIFFRACTIONp_scbond_it10.22
X-RAY DIFFRACTIONp_mcangle_it6.83
X-RAY DIFFRACTIONp_scangle_it11.32

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