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SMTL ID : 8q55.1

Ternary structure of 14-3-3s, C-RAF phosphopeptide (pS259) and compound 21 (1075354)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x GLN- ARG- SER- THR- SEP- THR- PRO- ASN- VAL: C-RAF peptide pS259(Non-covalent)

GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.1:

21 residues within 4Å:

Chain A: S.50, V.51, K.54, N.55, R.61, R.65, K.127, R.134, Y.135, G.176, L.179, N.180, V.183, Y.186, E.187, I.224, L.227, N.231, L.234, W.235
Ligands: JOL.6

18 PLIP interactions:

18 interactions with chain A

Hydrophobic interactions: A:L.179, A:L.227
Hydrogen bonds: A:V.51, A:K.54, A:R.61, A:N.180, A:N.180, A:E.187, A:N.231, A:N.231
Water bridges: A:K.54, A:K.54, A:N.55, A:R.61, A:R.61, A:R.61
Salt bridges: A:R.61, A:R.134

GLN-ARG-SER-THR-SEP-THR-PRO-ASN-VAL.7:

21 residues within 4Å:

Chain B: S.50, V.51, K.54, N.55, R.61, R.65, K.127, R.134, Y.135, G.176, L.179, N.180, V.183, Y.186, E.187, I.224, L.227, N.231, L.234, W.235
Ligands: JOL.12

20 PLIP interactions:

20 interactions with chain B

Hydrophobic interactions: B:L.179, B:L.227
Hydrogen bonds: B:V.51, B:R.61, B:Y.135, 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:K.54, B:N.55, B:R.61, B:R.61, B:R.61
Salt bridges: 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 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.94, H₂O.1, H₂O.2, H₂O.3, H₂O.8
MG.4:	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.2, H₂O.7
MG.5:	1 residues within 4Å: Chain A: E.193 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.193, H₂O.5
MG.9:	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.11, H₂O.12, H₂O.13, H₂O.18
MG.10:	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.12, H₂O.17
MG.11:	1 residues within 4Å: Chain B: E.193 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.193, H₂O.16

2 x JOL: 2-chloranyl-~{N}-[[1-(4-methylphenyl)sulfonylpiperidin-4-yl]methyl]ethanamide(Covalent)

JOL.6:	11 residues within 4Å: Chain A: C.43, E.44, N.47, K.127, P.172, I.173, G.176, 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.127, A:I.173 Water bridges: A:N.47, A:N.47
JOL.12:	11 residues within 4Å: Chain B: C.43, E.44, N.47, K.127, P.172, I.173, G.176, 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:K.127, B:I.173 Water bridges: B:N.47, B:N.47

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

2025-02-19

Peptides

14-3-3 protein sigma: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

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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