6V34 | pdb_00006v34

Crystal structure of BRAF V600E oncogenic mutant in complex with TAK-580

• PDB DOI: https://doi.org/10.2210/pdb6V34/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-11-25 Released: 2020-12-02 
• Deposition Author(s): Gonzalez Del-Pino, G., Li, K., Eck, M.J.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.286 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.258 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of BRAF V600E oncogenic mutant in complex with TAK-580

Gonzalez Del-Pino, G., Li, K., Eck, M.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

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: 65.1 kDa 
• Atom Count: 4,087 
• Modeled Residue Count: 503 
• Deposited Residue Count: 566 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase B-raf	A, B	283	Homo sapiens	Mutation(s): 15  Gene Names: BRAF 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QOP (Subject of Investigation/LOI)	C [auth A], D [auth B]	6-amino-5-chloro-N-[(1R)-1-(5-{[5-chloro-4-(trifluoromethyl)pyridin-2-yl]carbamoyl}-1,3-thiazol-2-yl)ethyl]pyrimidine-4-carboxamide C17 H12 Cl2 F3 N7 O2 S VWMJHAFYPMOMGF-ZCFIWIBFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
QOP	BindingDB:  6V34	IC50: min: 94, max: 633 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.286 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.258 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.802	α = 90
b = 85.244	β = 90
c = 122.905	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Gonzalez Del-Pino, G., Li, K., Eck, M.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P50 CA165962
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35 CA242461

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary