6AQ5

X-ray crystal structure of Erythrina crista-galli lectin in complex with epilactose

• PDB DOI: https://doi.org/10.2210/pdb6AQ5/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Erythrina crista-galli
• Mutation(s): No 


• Deposited: 2017-08-18 Released: 2018-08-22 
• Deposition Author(s): Gerlits, O., Woods, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.208 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Literature

X-ray crystal structure of Erythrina crista-galli lectin in complex with epilactose

Gerlits, O., Woods, R.J., Sood, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 54.62 kDa 
• Atom Count: 4,136 
• Modelled Residue Count: 478 
• Deposited Residue Count: 478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	A, B	239	Erythrina crista-galli	Mutation(s): 0
UniProt
Find proteins for Q6YD91 (Erythrina crista-galli) Explore Q6YD91  Go to UniProtKB:  Q6YD91

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-mannopyranose	C, E	2		N/A
Glycosylation Resources
GlyTouCan:  G40221BS GlyCosmos:  G40221BS GlyGen:  G40221BS

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-2)-[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	D	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G68461PT GlyCosmos:  G68461PT GlyGen:  G68461PT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MN	F [auth A], J [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	G [auth A], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.208 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.95	α = 90
b = 134.95	β = 90
c = 81.794	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Gerlits, O., Woods, R.J.

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary