2CIO | pdb_00002cio

The high resolution x-ray structure of papain complexed with fragments of the Trypanosoma brucei cysteine protease inhibitor ICP.

• PDB DOI: https://doi.org/10.2210/pdb2CIO/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Carica papaya, Trypanosoma brucei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-03-24 Released: 2006-05-18 
• Deposition Author(s): Alphey, M.S., Hunter, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.225 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

High-Resolution Complex of Papain with Remnants of a Cysteine Protease Inhibitor Derived from Trypanosoma Brucei

Alphey, M.S., Hunter, W.N.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 504

• PubMed: 16754967 
• DOI: https://doi.org/10.1107/S1744309106014849
• Primary Citation Related Structures: 
  2CIO


• PubMed Abstract: 
  

  Attempts to cocrystallize the cysteine protease papain derived from the latex of Carica papaya with an inhibitor of cysteine proteases (ICP) from Trypanosoma brucei were unsuccessful. However, crystals of papain that diffracted to higher resolution, 1.5 A, than other crystals of this archetypal cysteine protease were obtained, so the analysis was continued. Surprisingly, the substrate-binding cleft was occupied by two short peptide fragments which have been assigned as remnants of ICP. Comparisons reveal that these peptides bind in the active site in a manner similar to that of the human cysteine protease inhibitor stefin B when it is complexed to papain. The assignment of the fragment sequences is consistent with the specificity of the protease.

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Organizational Affiliation: 
• Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 37.31 kDa 
• Atom Count: 1,974 
• Modeled Residue Count: 219 
• Deposited Residue Count: 333 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PAPAIN	A	212	Carica papaya	Mutation(s): 0  EC: 3.4.22.2
UniProt
Find proteins for P00784 (Carica papaya) Explore P00784  Go to UniProtKB:  P00784

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
INHIBITOR OF CYSTEINE PEPTIDASE	B	121	Trypanosoma brucei	Mutation(s): 0
UniProt
Find proteins for Q868H0 (Trypanosoma brucei) Explore Q868H0  Go to UniProtKB:  Q868H0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth A], F [auth A], G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.225 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.323	α = 90
b = 46.118	β = 90
c = 95.697	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-18 
Deposition Author(s): Alphey, M.S., Hunter, W.N.

Revision History  

• Version 1.0: 2006-05-18
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-24
  Changes: Source and taxonomy
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description