2WO2

Crystal Structure of the EphA4-ephrinB2 complex

• PDB DOI: https://doi.org/10.2210/pdb2WO2/pdb

• Classification: TRANSFERASE/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2009-07-21 Released: 2009-10-27 
• Deposition Author(s): Bowden, T.A., Aricescu, A.R., Nettleship, J.E., Siebold, C., Rahman-Huq, N., Owens, R.J., Stuart, D.I., Jones, E.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.260 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 39.2 kDa 
• Atom Count: 2,596 
• Modelled Residue Count: 314 
• Deposited Residue Count: 338 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EPHRIN TYPE-A RECEPTOR	A	185	Homo sapiens	Mutation(s): 0  EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P54764 (Homo sapiens) Explore P54764  Go to UniProtKB:  P54764
PHAROS:  P54764 GTEx:  ENSG00000116106

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
EPHRIN-B2	B	153	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P52799 (Homo sapiens) Explore P52799  Go to UniProtKB:  P52799
PHAROS:  P52799 GTEx:  ENSG00000125266

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.260 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.371	α = 90
b = 107.371	β = 90
c = 47.619	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Bowden, T.A., Aricescu, A.R., Nettleship, J.E., Siebold, C., Rahman-Huq, N., Owens, R.J., Stuart, D.I., Jones, E.Y.

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-11-09
  Changes: Database references
• Version 1.3: 2018-02-28
  Changes: Source and taxonomy
• Version 1.4: 2020-07-01
  Changes: Data collection, Derived calculations, Other
• Version 1.5: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.6: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary