8XOX | pdb_00008xox

The Crystal Structure of FAK2 from Biortus.

• PDB DOI: https://doi.org/10.2210/pdb8XOX/pdb

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


• Deposited: 2024-01-02 Released: 2024-01-24 
• Deposition Author(s): Wang, F., Cheng, W., Lv, Z., Ju, C., Wang, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.230 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

The Crystal Structure of FAK2 from Biortus.

Wang, F., Cheng, W., Lv, Z., Ju, C., Wang, J.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.88 kDa 
• Atom Count: 2,392 
• Modeled Residue Count: 261 
• Deposited Residue Count: 277 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-tyrosine kinase 2-beta	A	277	Homo sapiens	Mutation(s): 0  Gene Names: PTK2B, FAK2, PYK2, RAFTK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14289 (Homo sapiens) Explore Q14289  Go to UniProtKB:  Q14289
PHAROS:  Q14289 GTEx:  ENSG00000120899

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YAM (Subject of Investigation/LOI)	B [auth A]	N-methyl-N-{3-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]pyridin-2-yl}methanesulfonamide C21 H20 F3 N7 O3 S MZDKLVOWGIOKTN-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
YAM	BindingDB:  8XOX	Ki: 1.5 (nM) from 1 assay(s)
		Kd: 5.7 (nM) from 1 assay(s)
		IC50: min: 1.4, max: 14 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.230 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.180 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.797	α = 90
b = 59.132	β = 95.033
c = 67.295	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-24 
Deposition Author(s): Wang, F., Cheng, W., Lv, Z., Ju, C., Wang, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-01-24
  Type: Initial release