2E9W

Crystal structure of the extracellular domain of Kit in complex with stem cell factor (SCF)

• PDB DOI: https://doi.org/10.2210/pdb2E9W/pdb

• Classification: TRANSFERASE/HORMONE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-01-27 Released: 2007-08-07 
• Deposition Author(s): Yuzawa, S., Opatowsky, Y., Zhang, Z., Mandiyan, V., Lax, I., Schlessinger, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.294 
• R-Value Work: 0.245 
• R-Value Observed: 0.245 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 143.24 kDa 
• Atom Count: 9,168 
• Modelled Residue Count: 1,197 
• Deposited Residue Count: 1,260 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mast/stem cell growth factor receptor	A, B	489	Homo sapiens	Mutation(s): 2  Gene Names: KIT EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P10721 (Homo sapiens) Explore P10721  Go to UniProtKB:  P10721
PHAROS:  P10721 GTEx:  ENSG00000157404

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Kit ligand	C, D	141	Homo sapiens	Mutation(s): 0  Gene Names: SCF
UniProt & NIH Common Fund Data Resources
Find proteins for P21583 (Homo sapiens) Explore P21583  Go to UniProtKB:  P21583
PHAROS:  P21583 GTEx:  ENSG00000049130

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.294 
• R-Value Work: 0.245 
• R-Value Observed: 0.245 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 269.477	α = 90
b = 52.072	β = 108
c = 189.791	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-07 
Deposition Author(s): Yuzawa, S., Opatowsky, Y., Zhang, Z., Mandiyan, V., Lax, I., Schlessinger, J.

Revision History  

• Version 1.0: 2007-08-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2021-11-10
  Changes: Database references, Structure summary
• Version 1.4: 2023-10-25
  Changes: Data collection, Refinement description