6YCF

Structure the bromelain protease from Ananas comosus in complex with the E64 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6YCF/pdb

• Classification: HYDROLASE
• Organism(s): Ananas comosus
• Mutation(s): No 


• Deposited: 2020-03-18 Released: 2020-11-25 
• Deposition Author(s): Azarkan, M., Charlier, P., Herman, R., Delbrassine, F., Sauvage, E., M Rabet, N., Calvo Esposito, R., Kerff, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.207 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.86 kDa 
• Atom Count: 3,882 
• Modelled Residue Count: 436 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FBSB	A, B	216	Ananas comosus	Mutation(s): 0
UniProt
Find proteins for A0A199VSS3 (Ananas comosus) Explore A0A199VSS3  Go to UniProtKB:  A0A199VSS3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G96987JC GlyCosmos:  G96987JC GlyGen:  G96987JC

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E64 (Subject of Investigation/LOI)	D [auth A], H [auth B]	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE C15 H30 N5 O5 QPQNJAXBPHVASB-QWRGUYRKSA-O
NAG	F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CIT	E [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
IPA	G [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.207 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.33	α = 90
b = 140.47	β = 90
c = 84.19	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Azarkan, M., Charlier, P., Herman, R., Delbrassine, F., Sauvage, E., M Rabet, N., Calvo Esposito, R., Kerff, F.

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description