SMTL ID : 6uxq.1 (1 other biounit)

Crystal structure of BAK core domain BH3-groove-dimer in complex with POPC and C8E4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.25 Chain B: R.25 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.25, A:R.25 SO4.2: 5 residues within 4Å: Chain A: Q.31, Q.35, H.78, Q.81, H.82 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.31, A:Q.35 Water bridges: A:R.74, A:H.78, A:Q.81 Salt bridges: A:H.78 SO4.10: 5 residues within 4Å: Chain B: Q.31, R.74, H.78, Q.81, H.82 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.31, B:Q.81, B:Q.81 Water bridges: B:Q.35 Salt bridges: B:R.74, B:H.78, B:H.82

6 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)

C8E.3: 2 residues within 4Å: Ligands: C8E.4, LBN.8 No protein-ligand interaction detected (PLIP) C8E.4: 7 residues within 4Å: Chain A: L.69, G.72, Y.73, A.76, L.77, Y.80 Ligands: C8E.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.73, A:A.76, A:Y.80 C8E.5: 3 residues within 4Å: Chain A: E.57, S.58 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.57 C8E.7: 10 residues within 4Å: Chain A: I.60, N.61, W.62, V.65 Chain B: N.23, D.27, L.69, Y.73, L.77 Ligands: C8E.11 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:W.62, A:V.65, B:L.69, B:Y.73, B:Y.73, B:Y.73, B:Y.73 Water bridges: A:W.62 Hydrogen bonds: B:N.23 C8E.9: 3 residues within 4Å: Chain B: F.56, L.68 Ligands: LBN.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.56, B:L.68 C8E.11: 8 residues within 4Å: Chain A: S.58, G.59, N.61, R.64 Chain B: D.20, N.23, R.24 Ligands: C8E.7 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.23, B:R.24 Water bridges: A:N.61, A:N.61

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

EDO.6: 2 residues within 4Å: Chain A: E.57 Ligands: C8E.5 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain B: S.6, T.7, M.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.7, B:M.8 EDO.13: 5 residues within 4Å: Chain B: G.4, S.5, S.6, G.9, R.13 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.4, B:G.4, B:S.5, B:S.6, B:S.6, B:R.13, B:R.13 Water bridges: B:Q.10

1 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)

LBN.8: 9 residues within 4Å: Chain A: L.69, Y.73 Chain B: I.60, N.61, W.62, V.65, L.69 Ligands: C8E.3, C8E.9 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.69, A:Y.73, B:I.60, B:W.62, B:V.65, B:V.65, B:L.69 Hydrogen bonds: A:Y.73, B:W.62 Water bridges: A:N.23

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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