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SMTL ID : 8s42.1

Ternary structure of 14-3-3s, C-RAF phosphopeptide (pS259) and compound 80 (1124898)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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:

18 residues within 4Å:

Chain A: 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: 01.5

21 PLIP interactions:

21 interactions with chain A

Hydrogen bonds: A:R.65, A:G.176, A:N.180, A:N.180, A:E.187, A:N.231, A:N.231
Water bridges: A:S.50, A:K.54, A:N.55, A:N.55, A:R.61, A:R.61, A:R.61, A:R.61, A:R.65, A:N.180, A:D.230
Salt bridges: A:K.54, A:R.61, A:R.134

GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.6:

18 residues within 4Å:

Chain B: 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: 01.10

24 PLIP interactions:

24 interactions with chain B

Hydrogen bonds: B:R.65, 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:S.50, 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, B:D.230
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.7:	4 residues within 4Å: Chain A: K.14 Chain B: E.88, Y.89, K.92 Ligand excluded by PLIP

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

MG.3:	1 residues within 4Å: Chain A: E.94 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.94, H₂O.2, H₂O.2, H₂O.7, H₂O.9
MG.4:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MG.8:	1 residues within 4Å: Chain B: E.94 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.94, H₂O.13, H₂O.13, H₂O.19, H₂O.21
MG.9:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x 01: 2-chloranyl-1-[8-[3-fluoranyl-4-(trifluoromethyl)phenyl]sulfonyl-5-oxa-2,8-diazaspiro[3.5]nonan-2-yl]ethanone

01.5:

15 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: 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

6 PLIP interactions:

6 interactions with chain A

Hydrophobic interactions: A:P.172, A:I.224
Hydrogen bonds: A:R.46
Water bridges: A:S.50, A:K.127
Halogen bonds: A:D.220

01.10:

15 residues within 4Å:

Chain B: 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: GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.6, GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.6, GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.6

6 PLIP interactions:

6 interactions with chain B

Hydrophobic interactions: B:P.172, B:I.224
Hydrogen bonds: B:R.46
Water bridges: B:S.50, B:K.127
Halogen bonds: B:D.220

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

2025-03-05

Peptides

14-3-3 protein sigma: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

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NGLPV2D

14-3-3 protein sigma

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