SMTL ID : 8spf.1

Crystal structure of Bax core domain BH3-groove dimer - hexameric fraction with 2-stearoyl lysoPC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

1 x 1GP: SN-GLYCEROL-1-PHOSPHATE(Non-covalent)

1GP.1: 3 residues within 4Å: Chain B: R.42 Chain E: N.59, W.60 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:R.42, E:W.60

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

EDO.2: 1 residues within 4Å: Chain B: S.71 No protein-ligand interaction detected (PLIP) EDO.3: 2 residues within 4Å: Chain C: P.41, R.42 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain B: F.58 Chain E: R.42, F.46 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.42 EDO.7: 3 residues within 4Å: Chain B: N.59, W.60 Chain E: R.42 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:W.60, E:R.42, E:R.42 EDO.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x OCT: N-OCTANE(Non-covalent)

OCT.5: 5 residues within 4Å: Chain E: F.67, A.70, S.71, V.74 Ligands: D12.6 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.67, E:V.74

1 x D12: DODECANE(Non-covalent)

D12.6: 5 residues within 4Å: Chain E: P.41, F.45, L.73, V.74 Ligands: OCT.5 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:P.41, E:F.45, E:F.45, E:F.45, E:L.73, E:V.74

1 x DD9: nonane(Non-covalent)

DD9.8: 6 residues within 4Å: Chain C: F.46, A.49, F.53 Chain F: R.42, F.46, A.49 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain F Hydrophobic interactions: C:F.46, C:A.49, C:F.53, F:R.42, F:F.46, F:A.49

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. (2024)

Release Date

2023-12-27

Peptides

Apoptosis regulator BAX: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
A

D
B

E
E

F
F

Apoptosis regulator BAX

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