6P3D: Serine/threonine-protein kinase B-raf

The co-crystal structure of BRAF(V600E) with ponatinib. Determined by X-ray diffraction at 2.11 Å resolution. Released 23 Sept 2020.

Method: X-ray diffraction
Resolution: 2.11 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,293
Mol. weight: 35.2 kDa
Ligands: 0LI
Released: 23 Sept 2020

Explore 6P3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6P3D contains 17 α-helices and 10 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	447-450	4
β-strand	451	1	1
α-helix	452-453	2
β-strand	458-466	9	1
β-strand	469-475	7	1
β-strand	479-484	6	1
α-helix	492-506	15
β-strand	513	1	2
β-strand	516-520	5	1
β-strand	526-530	5	1
α-helix	531-533	3
β-strand	534-536	3	2
α-helix	537-542	6
α-helix	550-569	20
α-helix	579-581	3
β-strand	582-585	4	2
β-strand	589-592	4	2
α-helix	597-599	3
α-helix	616-619	4
α-helix	622-626	5
α-helix	635-651	17
α-helix	662-671	10
α-helix	678-680	3
α-helix	687-696	10
α-helix	701-703	3
α-helix	705-706	2
α-helix	707-720	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase B-raf	A	protein	297	Homo sapiens	P15056 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6P3D_1 Serine/threonine-protein kinase B-raf (chains A)
MGSSHHHHHHSSGLVPRGSKMDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLN
VTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASET
KFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLATEKSRWSG
SHQFEQLSGSILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQII
EMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELARELSG

Ligands and cofactors

ID	Name	Formula	Copies
0LI	3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)…	C29 H27 F3 N6 O	1

Water and common crystallization additives (SO4, NH4, EDO) are not listed.

Primary citation

Inhibitors of BRAF dimers using an allosteric site. Cotto-Rios, X.M., Agianian, B., Gitego, N. et al. Nat Commun (2020) 11:4370-4370. DOI 10.1038/s41467-020-18123-2 · PubMed

Other PDB entries of the same protein (UniProt P15056 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8VSO 1.5 Å, Ternary structure of 14-3-3 sigma, BRAF phosphopeptide (pS365) and compound 78 (1124378)
8JNB 1.62 Å, CRAF ras-binding domain chimera, ligand complex
8C7X 1.65 Å, Crystal structure of BRAF in complex with a hybrid compound 6
8C7Y 1.65 Å, Crystal structure of BRAF V600E in complex with a hybrid compound 6
9EW6 1.65 Å, Binary structure of 14-3-3s and BRAF phosphopeptide (pS365)
8JNA 1.7 Å, CRAF ras-binding domain chimera, apo form
9BP8 1.73 Å, Crystal structure of BRAF kinase domain with PF-07799933
5VYK 1.75 Å, Crystal structure of the BRS domain of BRAF in complex with the CC-SAM domain of KSR1
9BFB 1.92 Å, Crystal structure of BRAF kinase domain with PF-07284890
7K0V 1.93 Å, Crystal structure of bRaf in complex with inhibitor GNE-0749
5ITA 1.95 Å, Crystal Structure of BRAF Kinase Domain Bound to AZ-VEM
3NY5 1.99 Å, Crystal structure of the RBD domain of serine/threonine-protein kinase B-raf from Homo…

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