3P1I | pdb_00003p1i

Ligand binding domain of human ephrin type-B receptor 3

• PDB DOI: https://doi.org/10.2210/pdb3P1I/pdb

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


• Deposited: 2010-09-30 Released: 2011-01-19 
• Deposition Author(s): Walker, J.R., Yermekbayeva, L., Seitova, A., Kania, J., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Ligand Binding Domain of Human Ephb3

Walker, J.R., Yermekbayeva, L., Seitova, A., Kania, J., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.52 kDa 
• Atom Count: 4,261 
• Modeled Residue Count: 502 
• Deposited Residue Count: 600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-B receptor 3	A, B, C	200	Homo sapiens	Mutation(s): 0  Gene Names: EPHB3, ETK2, HEK2, TYR06, TYRO6 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P54753 (Homo sapiens) Explore P54753  Go to UniProtKB:  P54753
PHAROS:  P54753 GTEx:  ENSG00000182580

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.235 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.16	α = 90
b = 102.16	β = 90
c = 117.86	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Walker, J.R., Yermekbayeva, L., Seitova, A., Kania, J., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-27
  Changes: Structure summary