SMTL ID : 8p0d.1

Human 14-3-3 sigma in complex with human MDM2 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: A.51, A.52, K.55, Y.76, G.122, V.123, T.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.76, A:Y.76, A:G.122, A:T.126 Water bridges: A:A.52 GOL.6: 7 residues within 4Å: Chain C: A.51, A.52, K.55, Y.76, G.122, V.123, T.126 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.76, C:Y.76, C:G.122, C:T.126 Water bridges: C:A.52

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 2 residues within 4Å: Chain A: E.114, T.118 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.114 Water bridges: A:E.114, A:E.117, A:E.117, A:E.117 PEG.7: 2 residues within 4Å: Chain C: E.114, T.118 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.114 Water bridges: C:T.118, C:T.118

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

CL.3: 6 residues within 4Å: Chain A: M.29, K.37, F.53 Chain C: E.111, Y.112, K.115 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain A: E.111, Y.112, K.115 Chain C: M.29, K.37, F.53 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 1 residues within 4Å: Chain A: E.30 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.30, H2O.3, H2O.7, H2O.12 MG.5: 4 residues within 4Å: Chain A: E.63, E.138, A.139, G.140 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.63, A:E.63, A:E.138, H2O.10, H2O.10 MG.9: 1 residues within 4Å: Chain C: E.30 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.30, H2O.17, H2O.22, H2O.26 MG.10: 4 residues within 4Å: Chain C: E.63, E.138, A.139, G.140 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.63, C:E.63, C:E.138, H2O.24, H2O.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ward, J.A. et al., Characterizing the protein-protein interaction between MDM2 and 14-3-3 sigma ; proof of concept for small molecule stabilization. J.Biol.Chem. (2024)

Release Date

2024-02-21

Peptides

14-3-3 protein sigma: AC
E3 ubiquitin-protein ligase Mdm2: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

14-3-3 protein sigma

E3 ubiquitin-protein ligase Mdm2