3ALU

Crystal structure of CEL-IV complexed with Raffinose

• PDB DOI: https://doi.org/10.2210/pdb3ALU/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Cucumaria echinata
• Mutation(s): No 


• Deposited: 2010-08-07 Released: 2011-01-19 
• Deposition Author(s): Hatakeyama, T., Hozawa, T., Ishii, K., Kamiya, T., Goda, S., Kusunoki, M., Unno, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.203 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 71.17 kDa 
• Atom Count: 5,734 
• Modelled Residue Count: 628 
• Deposited Residue Count: 628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin CEL-IV, C-type	A, B, C, D	157	Cucumaria echinata	Mutation(s): 0
UniProt
Find proteins for Q7M4F9 (Cucumaria echinata) Explore Q7M4F9  Go to UniProtKB:  Q7M4F9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose	E, F, G, H	3		N/A
Glycosylation Resources
GlyTouCan:  G40178VU GlyCosmos:  G40178VU

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	I [auth A], J [auth A], L [auth B], N [auth C], O [auth C], P [auth C], Q [auth C], S [auth D], T [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	K [auth A], M [auth B], R [auth C], U [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900002	E, F, G, H	raffinose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.203 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.808	α = 90
b = 78.159	β = 96.82
c = 102.883	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Hatakeyama, T., Hozawa, T., Ishii, K., Kamiya, T., Goda, S., Kusunoki, M., Unno, H.

Revision History  

• Version 1.0: 2011-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-05-30
  Changes: Non-polymer description
• Version 1.3: 2014-01-29
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary