1B5F

NATIVE CARDOSIN A FROM CYNARA CARDUNCULUS L.

• PDB DOI: https://doi.org/10.2210/pdb1B5F/pdb

• Classification: HYDROLASE
• Organism(s): Cynara cardunculus
• Mutation(s): No 


• Deposited: 1999-01-06 Released: 1999-01-13 
• Deposition Author(s): Frazao, C., Bento, I., Carrondo, M.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.256 
• R-Value Observed: 0.205 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 74.39 kDa 
• Atom Count: 5,842 
• Modelled Residue Count: 651 
• Deposited Residue Count: 652 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (CARDOSIN A)	A, C	239	Cynara cardunculus	Mutation(s): 0  EC: 3.4.23
UniProt
Find proteins for Q9XFX3 (Cynara cardunculus) Explore Q9XFX3  Go to UniProtKB:  Q9XFX3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (CARDOSIN A)	B, D	87	Cynara cardunculus	Mutation(s): 0  EC: 3.4.23
UniProt
Find proteins for Q9XFX3 (Cynara cardunculus) Explore Q9XFX3  Go to UniProtKB:  Q9XFX3

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-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	E	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G17689EW GlyCosmos:  G17689EW GlyGen:  G17689EW

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	F, H	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G18638YB GlyCosmos:  G18638YB GlyGen:  G18638YB

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[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	G	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G43648DB GlyCosmos:  G43648DB GlyGen:  G43648DB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.256 
• R-Value Observed: 0.205 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.964	α = 90
b = 87.186	β = 104.43
c = 81.303	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-01-13 
Deposition Author(s): Frazao, C., Bento, I., Carrondo, M.A.

Revision History  

• Version 1.0: 1999-01-13
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.0: 2020-09-23
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-08-09
  Changes: Data collection, Database references, Refinement description