5JSM: BRAFV600E Kinase Domain

BRAFV600E Kinase Domain In Complex with Chemically Linked Vemurafenib Inhibitor VEM-3-VEM. Determined by X-ray diffraction at 2.19 Å resolution. Released 14 Sept 2016.

Method: X-ray diffraction
Resolution: 2.19 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,786
Mol. weight: 130.68 kDa
Ligands: BEN, EOH, 6NB
Released: 14 Sept 2016

Explore 5JSM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5JSM contains 63 α-helices and 40 β-strands across 4 chains. 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: 15 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	451	1	1
β-strand	458-466	9	1
β-strand	469-475	7	1
β-strand	479-485	7	1
α-helix	492-507	16
β-strand	513	1	2
α-helix	514-515	2
β-strand	516-520	5	1
β-strand	526-530	5	1
β-strand	536	1	2
α-helix	537-539	3
α-helix	540-544	5
α-helix	550-569	20
α-helix	579-581	3
β-strand	582-584	3	2
β-strand	590-592	3	2
α-helix	615-619	5
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	707-719	13

Chain B: 18 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	447-450	4
β-strand	451	1	3
α-helix	452-453	2
β-strand	458-466	9	3
β-strand	469-475	7	3
β-strand	479-485	7	3
α-helix	492-507	16
β-strand	513	1	4
α-helix	514-515	2
β-strand	516-520	5	3
β-strand	526-530	5	3
β-strand	536	1	4
α-helix	537-538	2
α-helix	539-543	5
α-helix	550-569	20
α-helix	579-581	3
β-strand	582-584	3	4
β-strand	590-592	3	4
α-helix	598-601	4
α-helix	617-619	3
α-helix	622-625	4
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	707-719	13

Chain C: 14 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	451	1	5
α-helix	452-453	2
β-strand	458-466	9	5
β-strand	469-475	7	5
β-strand	479-485	7	5
α-helix	492-507	16
β-strand	513	1	6
α-helix	514-515	2
β-strand	516-520	5	5
β-strand	526-530	5	5
β-strand	536	1	6
α-helix	537-542	6
α-helix	550-569	20
α-helix	579-581	3
β-strand	582-584	3	6
β-strand	590-592	3	6
α-helix	622-625	4
α-helix	635-651	17
α-helix	664-670	7
α-helix	678-680	3
α-helix	687-696	10
α-helix	701-703	3
α-helix	705-706	2
α-helix	707-719	13

Chain D: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	447-450	4
β-strand	451	1	7
β-strand	458-466	9	7
β-strand	469-475	7	7
β-strand	479-485	7	7
α-helix	492-507	16
β-strand	513	1	8
α-helix	514-515	2
β-strand	516-520	5	7
β-strand	526-530	5	7
β-strand	536	1	8
α-helix	537-539	3
α-helix	540-544	5
α-helix	550-569	20
α-helix	579-581	3
β-strand	582-584	3	8
β-strand	590-592	3	8
α-helix	617-619	3
α-helix	622-625	4
α-helix	635-651	17
α-helix	664-671	8
α-helix	678-680	3
α-helix	687-696	10
α-helix	701-703	3
α-helix	705-706	2
α-helix	707-719	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase B-raf	A, B, C, D	protein	280	Homo sapiens	P15056 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5JSM_1 Serine/threonine-protein kinase B-raf (chains A, B, C, D)
GSEFDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVG
VLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARG
MDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLATEKSRWSGSHQFEQLSGSILWMAPE
VIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIEMVGRGSLSPDLSKVRS
NCPKRMKRLMAECLKKKRDERPSFPRILAEIEELARELSG

Ligands and cofactors

ID	Name	Formula	Copies
BEN	Benzamidine	C7 H8 N2	2
EOH	Ethanol	C2 H6 O	3
6NB	N,N'-{ethane-1,2-diylbis[oxyethane-2,1-diyloxy-4,1-phenylene-1H-pyrrolo[2,3-b]p…	C52 H48 F4 N6 O10 S2	2

Water and common crystallization additives (DMS, CL, GOL) are not listed.

Primary citation

Chemically Linked Vemurafenib Inhibitors Promote an Inactive BRAF(V600E) Conformation. Grasso, M., Estrada, M.A., Ventocilla, C. et al. ACS Chem Biol (2016) 11:2876-2888. DOI 10.1021/acschembio.6b00529 · 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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