SMTL ID : 6uxn.1 (5 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-dimer

Ligands

4 x 8SP: O-[(R)-{[(2R)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

8SP.1: 9 residues within 4Å: Chain A: I.60, N.61, W.62, V.65, V.66, L.69 Chain B: L.69, Y.73 Ligands: 8SP.5 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.69, B:Y.73, B:Y.73, B:Y.73, A:I.60, A:V.65, A:V.65, A:V.66 Hydrogen bonds: B:Y.73, A:W.62 8SP.2: 2 residues within 4Å: Chain A: T.32, H.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.32 Salt bridges: A:H.36 8SP.4: 7 residues within 4Å: Chain A: N.23, L.69, Y.73 Chain B: I.60, N.61, W.62, V.65 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:W.62, B:V.65, B:V.65, A:L.69, A:Y.73, A:Y.73, A:Y.73 Hydrogen bonds: B:W.62, A:N.23, A:Y.73 8SP.5: 12 residues within 4Å: Chain B: A.41, E.42, N.43, A.44, Y.45, E.46, F.48, L.69, G.72, Y.73, A.76 Ligands: 8SP.1 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.48, B:F.48, B:A.76 Hydrogen bonds: B:E.42, B:N.43, B:A.44, B:Y.45, B:E.46

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: Q.10, R.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.10 Salt bridges: A:R.13 SO4.6: 2 residues within 4Å: Chain A: R.25 Chain B: R.25 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.25 Water bridges: B:R.25, B:R.25 Salt bridges: B:R.25 SO4.7: 4 residues within 4Å: Chain B: T.7, G.9, Q.10, R.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.9 Salt bridges: B:R.13

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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