5KHW

Crystal structure of JAK1 in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb5KHW/pdb

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


• Deposited: 2016-06-16 Released: 2016-11-09 
• Deposition Author(s): Han, S., Caspers, N.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Literature

Development of a high-throughput crystal structure-determination platform for JAK1 using a novel metal-chelator soaking system.

Caspers, N.L., Han, S., Rajamohan, F., Hoth, L.R., Geoghegan, K.F., Subashi, T.A., Vazquez, M.L., Kaila, N., Cronin, C.N., Johnson, E., Kurumbail, R.G.

(2016) Acta Crystallogr F Struct Biol Commun 72: 840-845

• PubMed: 27827355 
• DOI: https://doi.org/10.1107/S2053230X16016356
• Primary Citation of Related Structures:  
  5KHW, 5KHX


• PubMed Abstract: 
  

  Crystals of phosphorylated JAK1 kinase domain were initially generated in complex with nucleotide (ADP) and magnesium. The tightly bound Mg ²⁺ -ADP at the ATP-binding site proved recalcitrant to ligand displacement. Addition of a molar excess of EDTA helped to dislodge the divalent metal ion, promoting the release of ADP and allowing facile exchange with ATP-competitive small-molecule ligands. Many kinases require the presence of a stabilizing ligand in the ATP site for crystallization. This procedure could be useful for developing co-crystallization systems with an exchangeable ligand to enable structure-based drug design of other protein kinases.

---

Organizational Affiliation: 

Structural Biology, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA.

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: 73.74 kDa 
• Atom Count: 4,665 
• Modelled Residue Count: 556 
• Deposited Residue Count: 632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK1	A, B	316	Homo sapiens	Mutation(s): 0  Gene Names: JAK1, JAK1A, JAK1B EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P23458 (Homo sapiens) Explore P23458  Go to UniProtKB:  P23458
PHAROS:  P23458 GTEx:  ENSG00000162434

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], E [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.631	α = 90
b = 146.62	β = 116.74
c = 49.936	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Han, S., Caspers, N.L.

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary