6EYJ

E-selectin lectin, EGF-like and two SCR domains complexed with glycomimetic ligand NV354

• PDB DOI: https://doi.org/10.2210/pdb6EYJ/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: 2.20 Å
• R-Value Free: 0.259 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

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.

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: 67.05 kDa 
• Atom Count: 4,894 
• Modelled Residue Count: 560 
• Deposited Residue Count: 560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E-selectin	A, B	280	Homo sapiens	Mutation(s): 0  Gene Names: SELE, ELAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P16581 (Homo sapiens) 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
C5H	J [auth A], S [auth B]	(2~{S})-3-cyclohexyl-2-[(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-3,5-bis(oxidanyl)-6-[(1~{R},2~{R})-2-[(2~{R},3~{S},4~{R},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(trifluoromethyl)oxan-2-yl]oxycyclohexyl]oxy-oxan-4-yl]oxy-propanoic acid C27 H43 F3 O13 OYWZGUHJADSZQK-NGNDWVCUSA-N
NAG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	K [auth A], T [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.259 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.58	α = 90
b = 71.04	β = 93.73
c = 92.16	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
DIALS	data reduction
Aimless	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
• Version 1.3: 2024-10-16
  Changes: Structure summary