7SHV | pdb_00007shv

Crystal structure of BRAF kinase domain bound to GDC0879

• PDB DOI: https://doi.org/10.2210/pdb7SHV/pdb

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


• Deposited: 2021-10-11 Released: 2022-10-26 
• Deposition Author(s): Kung, J.E., Sudhamsu, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 
  0.242 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Clearing the Path to Rapid High-Quality Protein Purification

Chen, X., Wendorff, T., Jao, C., Kung, J.E., Liau, N.P.D., Wu, P., Yu, C., Oh, A., Boenig, G., Wallweber, H., Everett, C., Miu, A., Brillantes, B., Mortara, K., Murray, J., Koth, C.M., Sudhamsu, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.4 kDa 
• Atom Count: 4,254 
• Modeled Residue Count: 523 
• Deposited Residue Count: 616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase B-raf	A, B	308	Homo sapiens	Mutation(s): 0  Gene Names: BRAF, BRAF1, RAFB1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens) Explore P15056  Go to UniProtKB:  P15056
PHAROS:  P15056 GTEx:  ENSG00000157764

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
29L (Subject of Investigation/LOI)	C [auth A], D [auth B]	2-{4-[(1E)-1-(hydroxyimino)-2,3-dihydro-1H-inden-5-yl]-3-(pyridin-4-yl)-1H-pyrazol-1-yl}ethanol C19 H18 N4 O2 DEZZLWQELQORIU-RELWKKBWSA-N
CL	E [auth B], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free:  0.242 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.638	α = 90
b = 98.638	β = 90
c = 159.136	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-26 
Deposition Author(s): Kung, J.E., Sudhamsu, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-10-26
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description