8JNB: CRAF ras-binding domain chimera, ligand complex

CRAF ras-binding domain chimera, ligand complex. Determined by X-ray diffraction at 1.62 Å resolution. Released 19 Jun 2024.

Method: X-ray diffraction
Resolution: 1.62 Å
Organism: Homo sapiens
Chains: 1
Atoms: 738
Mol. weight: 10.89 kDa
Ligands: USX
Released: 19 Jun 2024

Explore 8JNB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JNB contains 5 α-helices and 7 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 B: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	57-61	5	1
β-strand	67-71	5	1
β-strand	77	1	2
α-helix	78-87	10
α-helix	93-95	3
β-strand	96-101	6	1
β-strand	109-112	4	1
β-strand	117	1	2
α-helix	118-121	4
β-strand	125-130	6	1
α-helix	131-132	2
α-helix	135-138	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RAF proto-oncogene serine/threonine-protein kinase, CRaf	B	protein	94	Homo sapiens	P04049 (AlphaFold model), P15056 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8JNB_1 RAF proto-oncogene serine/threonine-protein kinase, CRaf (chains B)
GPLGSDPSKTSNTIRVFLPNSQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVYRLQDG
EKKPIGWNTDAAWLIGEELQVEFLDHVPLTTHNF

Ligands and cofactors

ID	Name	Formula	Copies
USX	2-[4-[[(2S)-1-ethanoyl-3-oxidanylidene-2H-indol-2-yl]methyl]-2-methoxy-phenoxy]…	C20 H20 N2 O5	1

Primary citation

Small-molecule RAS/RAF-binding Inhibitors Allosterically Disrupt RAF Conformation and Exert Efficacy Against Broad-spectrum RAS-driven Cancers. Yoshikawa, Y., Makino, Y., Kubota, H. et al. To be published.

Other PDB entries of the same protein (UniProt P04049 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3IQU 1.05 Å, Crystal Structure of human 14-3-3 sigma in Complex with Raf1 peptide (6mer)
3IQJ 1.15 Å, Crystal Structure of human 14-3-3 sigma in Complex with Raf1 peptide (10mer)
3IQV 1.2 Å, Crystal Structure of human 14-3-3 sigma in Complex with Raf1 peptide (6mer) and…
6VJJ 1.4 Å, Crystal Structure of wild-type KRAS4b (GMPPNP-bound) in complex with RAS-binding domain…
8ATS 1.4 Å, Small molecular stabilizer for C-RAF (pS259) and 14-3-3 (1075306)
9EW1 1.4 Å, Ternary structure of 14-3-3s, CRAF phosphopeptide (pS259) and compound 79 (1124379).
9EW3 1.4 Å, Ternary structure of 14-3-3s, C-RAF phosphopeptide 12-mer (pS259) and compound 78…
8AV0 1.5 Å, small molecule stabilizer (compound 1) for C-RAF pS259 and 14-3-3
9EW5 1.5 Å, Ternary structure of 14-3-3s, C-RAF phosphopeptide (pS259) 12mer and compound 23 (1083848)
9S2J 1.5 Å, Ternary structure of 14-3-3s, CRAF S257L NS mutant phosphopeptide (pS259) and compound…
9S2P 1.5 Å, Ternary structure of 14-3-3s, CRAF V263A NS mutant phosphopeptide (pS259), and compound…
8A68 1.6 Å, Small molecule stabilizer (compound 5) for C-RAF(pS259) and 14-3-3

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