6EYI

E-selectin lectin, EGF-like and two SCR domains complexed with glycomimetic ligand BW69669

• PDB DOI: https://doi.org/10.2210/pdb6EYI/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2017-11-13 Released: 2018-11-21 
• Deposition Author(s): Jakob, R.P., Zihlmann, P., Preston, R.C., Varga, N., Ernst, B., Maier, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.237 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 

Starting Model: experimental

Literature

E-selectin lectin with different glycomimetic ligands

Varga, N., Zihlmann, P., Preston, R.C., Jakob, R.P., Maier, T., Ernst, B.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 33.55 kDa 
• Atom Count: 2,448 
• Modelled Residue Count: 280 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E-selectin	A	280	Homo sapiens	Mutation(s): 0  Gene Names: SELE, ELAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P16581 (Homo sapiens) Explore P16581  Go to UniProtKB:  P16581
PHAROS:  P16581 GTEx:  ENSG00000007908
Glycosylation
Glycosylation Sites: 7		Go to GlyGen: P16581-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C4Z	I [auth A]	(2~{R})-3-cyclohexyl-2-[(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(1~{R},2~{R})-2-[(2~{S},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxycyclohexyl]oxy-3,5-bis(oxidanyl)oxan-4-yl]oxy-propanoic acid C27 H46 O13 GNTJIZLFEURZBX-AUCBMRIBSA-N
NAG	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	J [auth A], K [auth A], L [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.237 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.59	α = 90
b = 72.94	β = 94.16
c = 52.52	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Jakob, R.P., Zihlmann, P., Preston, R.C., Varga, N., Ernst, B., Maier, T.

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary