3KUL | pdb_00003kul

Kinase domain of human ephrin type-A receptor 8 (EPHA8)

• PDB DOI: https://doi.org/10.2210/pdb3KUL/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-11-27 Released: 2009-12-15 
• Deposition Author(s): Walker, J.R., Yermekbayeva, L., Kania, J., Bountra, C., Weigelt, J., 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: 2.15 Å
• R-Value Free: 
  0.244 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Kinase Domain of Human Ephrin Type-A Receptor 8 (Epha8)

Walker, J.R., Yermekbayeva, L., 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)

Macromolecule Content 

• Total Structure Weight: 73.92 kDa 
• Atom Count: 4,538 
• Modeled Residue Count: 539 
• Deposited Residue Count: 650 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-A receptor 8	A	325	Homo sapiens	Mutation(s): 0  Gene Names: EEK, EPHA8, HEK3, KIAA1459 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29322 (Homo sapiens) Explore P29322  Go to UniProtKB:  P29322
PHAROS:  P29322 GTEx:  ENSG00000070886

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-A receptor 8	B	325	Homo sapiens	Mutation(s): 0  Gene Names: EEK, EPHA8, HEK3, KIAA1459 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29322 (Homo sapiens) Explore P29322  Go to UniProtKB:  P29322
PHAROS:  P29322 GTEx:  ENSG00000070886

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME	D [auth A], G [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.244 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.14	α = 90
b = 41.879	β = 92.46
c = 145.815	γ = 90

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: 2009-12-15 
Deposition Author(s): Walker, J.R., Yermekbayeva, L., 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: 2009-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-22
  Changes: Data collection