SMTL ID : 8qsg.1

Ternary structure of 14-3-3s, BRAF phosphopeptide (pS365) and compound 86 (1124384).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x ASP- ARG- SER- SER- SEP- ALA- PRO- ASN- VAL: BRAF peptide pS365(Non-covalent)

ASP-ARG-SER-SER-SEP-ALA-PRO-ASN-VAL.1: 21 residues within 4Å: Chain A: N.47, V.51, K.54, N.55, R.61, R.65, R.134, Y.135, L.179, N.180, V.183, Y.186, E.187, K.219, D.220, L.223, L.227, N.231, L.234, W.235 Ligands: WQ9.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.223 Hydrogen bonds: A:N.47, A:N.55, A:Y.135, A:N.180, A:E.187, A:E.187, A:N.231, A:N.231 Water bridges: A:S.50, A:K.54, A:R.61, A:R.61, A:R.61, A:R.61, A:R.61, A:N.180, A:N.180 Salt bridges: A:K.54, A:R.61, A:R.134 ASP-ARG-SER-SER-SEP-ALA-PRO-ASN-VAL.2: 20 residues within 4Å: Chain B: N.47, V.51, K.54, N.55, R.61, R.65, R.134, Y.135, L.179, N.180, V.183, Y.186, E.187, D.220, L.223, L.227, N.231, L.234, W.235 Ligands: WQ9.8 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.223 Hydrogen bonds: B:N.55, B:N.55, B:N.180, B:E.187, B:N.231, B:N.231 Water bridges: B:K.54, B:R.61, B:R.61, B:R.65, B:R.65, B:N.180, B:N.180 Salt bridges: B:K.54, B:R.61, B:R.134

2 x WQ9: 1-[(5~{R})-2-(4-bromanyl-3-fluoranyl-phenyl)sulfonyl-2,7-diazaspiro[4.4]nonan-7-yl]-2-chloranyl-ethanone(Covalent)

WQ9.3: 14 residues within 4Å: Chain A: C.43, R.46, N.47, S.50, E.120, F.124, K.127, P.172, I.173, D.220, L.223, I.224 Ligands: ASP-ARG-SER-SER-SEP-ALA-PRO-ASN-VAL.1, ASP-ARG-SER-SER-SEP-ALA-PRO-ASN-VAL.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.124, A:I.173 Hydrogen bonds: A:R.46 Water bridges: A:S.50, A:D.131, A:N.180 WQ9.8: 13 residues within 4Å: Chain B: C.43, R.46, N.47, S.50, F.124, K.127, P.172, I.173, D.220, I.224 Ligands: ASP-ARG-SER-SER-SEP-ALA-PRO-ASN-VAL.2, ASP-ARG-SER-SER-SEP-ALA-PRO-ASN-VAL.2, ASP-ARG-SER-SER-SEP-ALA-PRO-ASN-VAL.2 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.124, B:I.173 Hydrogen bonds: B:R.46 Water bridges: B:N.180

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 1 residues within 4Å: Chain A: E.94 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.94, H2O.2, H2O.5 MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain A: K.37 No protein-ligand interaction detected (PLIP) MG.10: 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.7, H2O.9, H2O.10 MG.11: 2 residues within 4Å: Chain B: S.79, E.81 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: E.7 No protein-ligand interaction detected (PLIP)

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

CL.7: 3 residues within 4Å: Chain A: K.14 Chain B: Y.89, K.92 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: E.88, Y.89 Chain B: K.14 Ligand excluded by PLIP

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

2025-04-23

Peptides

14-3-3 protein sigma: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
J

14-3-3 protein sigma

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