SMTL ID : 9ew1.1

Ternary structure of 14-3-3s, CRAF phosphopeptide (pS259) and compound 79 (1124379).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x GLN- ARG- SER- THR- SEP- THR- PRO- ASN- VAL: RAF proto-oncogene serine/threonine-protein kinase(Non-covalent)

GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.1: 19 residues within 4Å: Chain A: N.47, V.51, K.54, N.55, R.61, R.65, R.134, Y.135, G.176, L.179, N.180, V.183, Y.186, E.187, L.227, N.231, L.234, W.235 Ligands: WQT.6 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:N.47, A:N.55, A:G.176, A:N.180, A:N.180, A:E.187, A:N.231, A:N.231 Water bridges: A:N.47, A:K.54, A:N.55, A:R.61, A:R.61, A:R.61, A:R.61, A:R.65, A:N.180 Salt bridges: A:K.54, A:R.61, A:R.134 GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.7: 19 residues within 4Å: Chain B: N.47, V.51, K.54, N.55, R.61, R.65, R.134, Y.135, G.176, L.179, N.180, V.183, Y.186, E.187, L.227, N.231, L.234, W.235 Ligands: WQT.12 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:N.47, B:Y.135, B:N.180, B:N.180, B:N.180, B:E.187, B:E.187, B:N.231, B:N.231, B:N.231 Water bridges: B:K.54, B:N.55, B:N.55, B:R.61, B:R.61, B:R.61, B:R.61, B:R.65, B:N.180 Salt bridges: B:K.54, B:R.61, B:R.134

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: E.88, Y.89, K.92 Chain B: K.14 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: K.14 Chain B: E.88, Y.89, K.92 Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: E.94 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.94, H2O.1, H2O.2, H2O.8 MG.4: 1 residues within 4Å: Chain A: E.80 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.80 MG.5: 1 residues within 4Å: Chain A: E.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.7, H2O.1, H2O.5 MG.9: 1 residues within 4Å: Chain B: E.94 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.94, H2O.10, H2O.12, H2O.17 MG.10: 1 residues within 4Å: Chain B: E.80 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.80 MG.11: 1 residues within 4Å: Chain B: E.7 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.7, H2O.11, H2O.14

2 x WQT: 2-chloranyl-1-[8-(4-iodophenyl)sulfonyl-5-oxa-2,8-diazaspiro[3.5]nonan-2-yl]ethanone(Covalent)

WQT.6: 14 residues within 4Å: Chain A: C.43, R.46, N.47, S.50, E.120, F.124, K.127, P.172, I.173, L.223, I.224 Ligands: GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.1, GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.1, GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.224 Hydrogen bonds: A:R.46 Water bridges: A:K.127 WQT.12: 14 residues within 4Å: Chain B: C.43, R.46, N.47, S.50, E.120, F.124, K.127, P.172, I.173, L.223, I.224 Ligands: GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.7, GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.7, GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.7 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.224 Hydrogen bonds: B:R.46 Water bridges: B:K.127, B:D.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Konstantinidou, M. et al., Small molecule stabilization of the 14-3-3sigma/CRAF complex inhibits the MAPK pathway. To Be Published

Release Date

2025-04-16

Peptides

14-3-3 protein sigma: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

14-3-3 protein sigma

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