3HIL | pdb_00003hil

SAM Domain of Human Ephrin Type-A Receptor 1 (EphA1)

• PDB DOI: https://doi.org/10.2210/pdb3HIL/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-20 Released: 2009-06-09 
• Deposition Author(s): Walker, J.R., Yermekbayeva, L., Butler-Cole, C., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.279 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

SAM Domain of Human Ephrin Type-A Receptor 1 (EphA1).

Walker, J.R., Yermekbayeva, L., Butler-Cole, C., Weigelt, J., Bountra, C., 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)

Macromolecule Content 

• Total Structure Weight: 19.22 kDa 
• Atom Count: 1,069 
• Modeled Residue Count: 125 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-A receptor 1	A, B	82	Homo sapiens	Mutation(s): 0  Gene Names: EPH, EPHA1, EPHT, EPHT1, MGC163163 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P21709 (Homo sapiens) Explore P21709  Go to UniProtKB:  P21709
PHAROS:  P21709 GTEx:  ENSG00000146904

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	D [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.279 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.286	α = 90
b = 52.286	β = 90
c = 81.307	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-09 
Deposition Author(s): Walker, J.R., Yermekbayeva, L., Butler-Cole, C., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-06-09
  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