SMTL ID : 8srx.1

Crystal structure of BAK-BAX heterodimer with lysoPC

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

hetero-2-2-mer

Ligands

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

K6G.1: 16 residues within 4Å: Chain A: A.41, A.44, Y.45, G.72, Y.73, A.76, V.79, Y.80 Chain C: W.62, V.65, V.66, L.69 Chain D: F.66, S.70, L.74 Ligands: CL.11 14 PLIP interactions: 5 interactions with chain C, 5 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: C:W.62, C:W.62, C:V.65, C:V.66, A:A.44, A:Y.45, A:Y.45, A:A.76, D:F.66, D:F.66 Water bridges: C:W.62, D:K.71, D:K.71 Hydrogen bonds: A:Y.45 K6G.4: 16 residues within 4Å: Chain A: W.62, V.65, V.66, L.69 Chain B: Q.29, F.66, S.70, K.71, L.74 Chain C: A.44, Y.45, G.72, Y.73, A.76, V.79, Y.80 13 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: C:Y.45, C:Y.73, A:W.62, A:V.65, A:V.66, B:F.66, B:F.66 Hydrogen bonds: C:Y.45, C:Y.45, C:A.76 Water bridges: A:W.62, B:K.71 Salt bridges: B:K.71 K6G.7: 16 residues within 4Å: Chain B: F.44, F.66, A.69, V.73, A.76, L.77, T.79, K.80 Chain D: F.52, G.55, N.56, F.57, L.65, F.66 Ligands: PEG.5, EDO.10 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:F.44, B:F.66, B:A.69, B:V.73, B:V.73, B:A.76, B:L.77, D:F.52, D:L.65, D:F.66 Hydrogen bonds: B:T.79, B:T.79

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: H.78, H.82 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.78, A:H.82, H2O.1

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 1 residues within 4Å: Chain A: Q.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.35 NA.6: 1 residues within 4Å: Chain B: K.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.9, B:K.9

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

PEG.5: 8 residues within 4Å: Chain B: R.41, V.73, A.76 Chain D: F.44, A.48, F.52 Ligands: K6G.7, EDO.10 No protein-ligand interaction detected (PLIP) PEG.8: 2 residues within 4Å: Chain B: F.52 Chain D: L.77 No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 6 residues within 4Å: Chain B: F.44 Chain D: P.40, R.41, F.44, V.73, A.76 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain D: A.49, F.52 Ligands: PEG.5, K6G.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.52

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

CL.11: 4 residues within 4Å: Chain A: Y.80 Chain D: K.71, L.74 Ligands: K6G.1 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, M.S. et al., Sequence differences between BAX and BAK core domains manifest as differences in their interactions with lipids. Febs J. (2023)

Release Date

2023-12-27

Peptides

Bcl-2 homologous antagonist/killer: AC
Apoptosis regulator BAX: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Bcl-2 homologous antagonist/killer

Apoptosis regulator BAX

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