2X10

Crystal structure of the complete EphA2 ectodomain

• PDB DOI: https://doi.org/10.2210/pdb2X10/pdb

• Classification: RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2009-12-21 Released: 2010-03-16 
• Deposition Author(s): Seiradake, E., Harlos, K., Sutton, G., Aricescu, A.R., Jones, E.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.299 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 60.68 kDa 
• Atom Count: 3,743 
• Modelled Residue Count: 485 
• Deposited Residue Count: 545 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EPHRIN TYPE-A RECEPTOR 2	A	545	Homo sapiens	Mutation(s): 0  EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29317 (Homo sapiens) Explore P29317  Go to UniProtKB:  P29317
PHAROS:  P29317 GTEx:  ENSG00000142627

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.299 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.92	α = 93.02
b = 44.65	β = 98.22
c = 93.42	γ = 112.12

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
MOSFLM	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-16 
Deposition Author(s): Seiradake, E., Harlos, K., Sutton, G., Aricescu, A.R., Jones, E.Y.

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2013-01-30
  Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
• Version 1.2: 2018-02-28
  Changes: Source and taxonomy
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary