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- PDB-1ppd: RESTRAINED LEAST-SQUARES REFINEMENT OF THE SULFHYDRYL PROTEASE PA... -

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Basic information

Entry
Database: PDB / ID: 1ppd
TitleRESTRAINED LEAST-SQUARES REFINEMENT OF THE SULFHYDRYL PROTEASE PAPAIN TO 2.0 ANGSTROMS
Components2-HYDROXYETHYL-THIOPAPAIN
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
BETA-MERCAPTOETHANOL / Papain
Similarity search - Component
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsJansonius, J.N.
Citation
Journal: Acta Crystallogr.,Sect.A / Year: 1984
Title: Restrained Least-Squares Refinement of the Sulfhydryl Protease Papain to 2.0 Angstroms
Authors: Priestle, J.P. / Ford, G.C. / Glor, M. / Mehler, E.L. / Smit, J.D.G. / Thaller, C. / Jansonius, J.N.
History
DepositionNov 6, 1984Processing site: BNL
Revision 1.0Jan 2, 1985Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-HYDROXYETHYL-THIOPAPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5272
Polymers23,4491
Non-polymers781
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.800, 95.700, 49.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE CYS 25, THE ACTIVE SULPHYDRYL IS INHIBITED WITH 2-MERCAPTOETHANOL
2: RESIDUE 152 IS A CIS PROLINE.
3: ILE 34 HAS A SECOND, LESS OCCUPIED, SIDE CHAIN CONFORMATION WHICH IS NOT INCLUDED IN THIS LIST.

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Components

#1: Protein 2-HYDROXYETHYL-THIOPAPAIN


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-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE CYS 25, THE ACTIVE SULPHYDRYL IS INHIBITED WITH 2-MERCAPTOETHANOL
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.3 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→10 Å
Details: THE CRYSTALS USED ARE OF THE *D* TYPE, COURTESY OF PROF. J. DRENTH OF THE UNIVERSITY OF GRONINGEN, GRONINGEN, THE NETHERLANDS.
RfactorNum. reflection
obs0.145 13394
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1655 0 0 215 1870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_deg1.9

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