8TV1

Structure of the EphA2 LBDCRD bound to FabS1C_L1

• PDB DOI: https://doi.org/10.2210/pdb8TV1/pdb

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


• Deposited: 2023-08-17 Released: 2024-06-26 
• Deposition Author(s): Singer, A.U., Bruce, H.A., Blazer, L., Adams, J.J., Sicheri, F., Sidhu, S.S.
• Funding Organization(s): Celgene Corporation, Bristol-Myers Squibb (BMS) Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.246 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Starting Models: experimental

Literature

Synthetic Antibodies targeting EPHA2 Induce Diverse Signaling-Competent Clusters with Differential Activation

Adams, J.J., Bruce, H.A., Ploder, L., Garcia, J., Khutoreskaya, G., Jarvik, N., Costa, L.E., Gorelik, M., Pot, I., Sicheri, F., Blazer, L.L., Singer, A.U., Sidhu, S.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 82.2 kDa 
• Atom Count: 5,620 
• Modelled Residue Count: 743 
• Deposited Residue Count: 756 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S1C variant of Fab_L1 heavy chain	A [auth D]	237	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S1C variant of Fab_L1 light chain	B [auth E]	211	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-A receptor 2	C	308	Homo sapiens	Mutation(s): 0  Gene Names: EPHA2, ECK 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
EDO (Subject of Investigation/LOI)	E	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	D, F [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.246 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.437	α = 90
b = 73.249	β = 107.43
c = 118.57	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Singer, A.U., Bruce, H.A., Blazer, L., Adams, J.J., Sicheri, F., Sidhu, S.S.

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Funding Organization	Location	Grant Number
Celgene Corporation	United States	Operating Contract
Bristol-Myers Squibb (BMS) Research	United States	Collaboration and Option Agreement

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release