SMTL ID : 6uxr.1

Crystal structure of BAK core domain BH3-groove-dimer in complex with LysoPC

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x K6G: [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] hexadecanoate(Non-covalent)

K6G.1: 6 residues within 4Å: Chain A: I.60, W.62, V.65 Chain B: L.69, Y.73 Ligands: PGE.7 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.62, A:V.65, A:V.65, B:L.69, B:L.69, B:Y.73, B:Y.73 Water bridges: A:I.60 K6G.2: 5 residues within 4Å: Chain A: L.69, Y.73 Chain B: I.60, W.62 Ligands: PG4.3 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.60, B:I.60, B:W.62, A:Y.73, A:Y.73

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 5 residues within 4Å: Chain B: A.52, T.53, V.65 Ligands: K6G.2, PGE.4 No protein-ligand interaction detected (PLIP)

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 4 residues within 4Å: Chain B: F.56, I.60 Ligands: PG4.3, PGE.5 No protein-ligand interaction detected (PLIP) PGE.5: 1 residues within 4Å: Ligands: PGE.4 No protein-ligand interaction detected (PLIP) PGE.6: 3 residues within 4Å: Chain B: Y.73, R.74, L.77 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.73, B:R.74, B:R.74 PGE.7: 5 residues within 4Å: Chain B: L.69, G.72, Y.73, L.75 Ligands: K6G.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cowan, A.D. et al., BAK core dimers bind lipids and can be bridged by them. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-09-02

Peptides

Bcl-2 homologous antagonist/killer: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bcl-2 homologous antagonist/killer

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