SMTL ID : 6fnb.1

Mono- and bivalent 14-3-3 inhibitors for characterizing supramolecular lysine-PEG interactions in proteins

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.1: 4 residues within 4Å: Chain A: F.196, M.218, Q.219, R.222 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.196, A:Q.219 Salt bridges: A:R.222 BEZ.7: 4 residues within 4Å: Chain B: F.196, M.218, Q.219, R.222 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.196, B:Q.219 Salt bridges: B:R.222

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: D.197, R.222, L.225 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.197, A:R.222 GOL.8: 4 residues within 4Å: Chain A: K.9, D.21, C.25 Chain B: Y.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.21 GOL.9: 2 residues within 4Å: Chain A: K.75 Chain B: K.11 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: Y.19, D.20 Ligands: CL.4, CL.5 No protein-ligand interaction detected (PLIP) CA.10: 3 residues within 4Å: Chain B: D.20 Ligands: CL.11, CL.12 No protein-ligand interaction detected (PLIP)

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

CL.4: 5 residues within 4Å: Chain A: R.18, Y.19, D.20, D.21 Ligands: CA.3 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: E.17, Y.19 Ligands: CA.3 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: R.18, Y.19, D.20, D.21 Ligands: CA.10 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: E.17, Y.19 Ligands: CA.10 Ligand excluded by PLIP

2 x DWQ: [2-[2-oxidanylidene-2-[[3-[2-[5-[3-oxidanylidene-3-[3-[2-[2-[3-[3-[2-[2-[2-[[3-[2-(2-phosphonophenoxy)ethanoylamino]phenyl]carbonylamino]ethoxy]ethoxy]ethoxy]propanoylamino]propoxy]ethoxy]ethoxy]propylamino]propoxy]pentoxy]ethylcarbamoyl]phenyl]amino]ethoxy]phenyl]phosphonic acid(Non-covalent)

DWQ.6: 9 residues within 4Å: Chain A: K.49, N.50, G.53, R.56, R.60, R.127, Y.128, N.173, L.220 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.220 Hydrogen bonds: A:K.49, A:G.53, A:R.56, A:R.56, A:R.60, A:R.127, A:R.127, A:Y.128, A:Y.128, A:Y.128 Water bridges: A:R.60, A:N.173 pi-Cation interactions: A:R.56 DWQ.13: 11 residues within 4Å: Chain B: K.49, N.50, G.53, R.56, R.60, R.127, Y.128, L.172, N.173, V.176, L.220 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.172, B:V.176 Hydrogen bonds: B:K.49, B:G.53, B:R.56, B:R.56, B:R.127, B:R.127, B:Y.128, B:Y.128 Water bridges: B:N.173 pi-Cation interactions: B:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yilmaz, E. et al., Mono- and Bivalent 14-3-3 Inhibitors for Characterizing Supramolecular "Lysine Wrapping" of Oligoethylene Glycol (OEG) Moieties in Proteins. Chemistry (2018)

Release Date

2018-07-04

Peptides

14-3-3 protein zeta/delta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

14-3-3 protein zeta/delta

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