SMTL ID : 6fnc.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

2 x DWK: [2-[2-oxidanylidene-2-[[3-[3-[2-[2-[3-[[4-[2-(2-phosphonophenoxy)ethanoylamino]phenyl]carbonylamino]propoxy]ethoxy]ethoxy]propylcarbamoyl]phenyl]amino]ethoxy]phenyl]phosphonic acid(Non-covalent)

DWK.1: 11 residues within 4Å: Chain A: K.49, N.50, G.53, R.56, R.60, R.127, Y.128, L.172, N.173, I.217, L.220 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.172 Hydrogen bonds: A:K.49, A:R.56, A:R.56, A:R.127, A:R.127, A:Y.128, A:Y.128, A:Y.128 Water bridges: A:G.53, A:R.60, A:N.173 pi-Cation interactions: A:R.56 DWK.7: 10 residues within 4Å: Chain B: K.49, N.50, G.53, R.56, R.127, Y.128, L.172, N.173, V.176, L.220 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.172, B:V.176, B:L.220 Hydrogen bonds: B:K.49, B:R.56, B:R.56, B:R.60, B:R.127, B:R.127, B:Y.128, B:Y.128 Water bridges: B:G.53, B:Y.128, B:N.173 pi-Cation interactions: B:R.56

2 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.2: 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.8: 4 residues within 4Å: Chain B: F.196, M.218, Q.219, R.222 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.222

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: Y.82 Chain B: K.9, C.25 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.78 GOL.9: 3 residues within 4Å: Chain A: K.9 Chain B: Y.82, K.85 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: Y.19 Ligands: CL.5, CL.6 No protein-ligand interaction detected (PLIP) CA.10: 4 residues within 4Å: Chain B: Y.19, D.20 Ligands: CL.11, CL.12 No protein-ligand interaction detected (PLIP)

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

CL.5: 5 residues within 4Å: Chain A: R.18, Y.19, D.20, D.21 Ligands: CA.4 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: E.17, Y.19 Ligands: CA.4 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

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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