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- PDB-1pop: X-RAY CRYSTALLOGRAPHIC STRUCTURE OF A PAPAIN-LEUPEPTIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1pop
TitleX-RAY CRYSTALLOGRAPHIC STRUCTURE OF A PAPAIN-LEUPEPTIN COMPLEX
Components
  • LEUPEPTIN
  • PAPAIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
LEUPEPTIN / METHANOL / : / Papain
Similarity search - Component
Biological speciesCarica papaya (papaya)
Streptomyces roseus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsSchroder, E. / Crawford, C.
Citation
Journal: FEBS Lett. / Year: 1993
Title: X-ray crystallographic structure of a papain-leupeptin complex.
Authors: Schroder, E. / Phillips, C. / Garman, E. / Harlos, K. / Crawford, C.
#1: Journal: J.Mol.Biol. / Year: 1984
Title: The Structure of Papain Refined at 1.65 Angstroms
Authors: Kamphuis, I.G. / Kalk, K.H. / Swarte, M.B.A. / Drenth, J.
History
DepositionJun 24, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Apr 2, 2014Group: Source and taxonomy
Revision 1.5Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.6Oct 23, 2024Group: 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PAPAIN
B: LEUPEPTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,64826
Polymers23,8792
Non-polymers76924
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-20 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.920, 104.960, 50.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 152
2: THE LEUPEPTIN MOLECULE, CHAIN *B*, IS COVALENTLY ATTACHED TO CYS 25.

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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: Protein/peptide LEUPEPTIN


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 429.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces roseus (bacteria) / Strain: MA 839-A1 / References: NOR: NOR00487, LEUPEPTIN
#3: Chemical...
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: CH4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE LEUPEPTIN IS COVALENTLY CONNECTED TO ACTIVE_SITE CYS 25 OF THE ENZYME TO FORM A HEMITHIOACETAL.
Has protein modificationY
Sequence detailsTHERE IS A DISCREPANCY IN THE NORINE AND PDB NUMBERING, AS NORINE COUNTS ACE AND LEU TOGETHER AS ...THERE IS A DISCREPANCY IN THE NORINE AND PDB NUMBERING, AS NORINE COUNTS ACE AND LEU TOGETHER AS ONE RESIDUE. SO THE DBREF WILL REPORT 4 PDB RESIDUES MATCHING NORINE 3 RESIDUE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-IDDetailsChemical formula
1H2O-methanol1reservoir0.5ml
3inhibited papain1drop0.030ml
21reservoir0.060mlsatNaCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 12452 / % possible obs: 88 % / Rmerge(I) obs: 0.094

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementHighest resolution: 2.1 Å / σ(F): 2
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 0 48 175 1908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.33
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS

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