SMTL ID : 6uxo.2 (5 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.1: 13 residues within 4Å: Chain A: I.60, N.61, W.62, V.65, L.69 Chain B: N.23, L.69, Y.73, L.77, Q.81 Ligands: LMT.7, LMT.10, SO4.11 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.69, B:Y.73, B:Y.73, B:Y.73, A:V.65, A:V.65, A:L.69 Hydrogen bonds: B:N.23, B:Y.73, B:Q.81, B:Q.81, A:W.62 Water bridges: B:D.27, B:R.74 LMT.7: 12 residues within 4Å: Chain A: N.23, D.27, L.69, Y.73, R.74 Chain B: I.60, N.61, W.62, V.65, L.69 Ligands: LMT.1, SO4.9 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.69, A:Y.73, A:Y.73, B:W.62, B:V.65 Hydrogen bonds: A:N.23, A:N.23, A:Y.73, A:R.74, A:R.74 Water bridges: B:N.61, B:W.62 LMT.8: 3 residues within 4Å: Chain A: H.36 Chain B: T.7 Ligands: SO4.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.7 Water bridges: B:Q.10 Salt bridges: A:H.36 LMT.10: 4 residues within 4Å: Chain B: Y.45, F.48, G.72 Ligands: LMT.1 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.45, B:F.48, B:F.48, B:F.48

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

SO4.2: 4 residues within 4Å: Chain A: Q.31, R.74, H.78, H.82 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.31 Water bridges: A:Q.81 Salt bridges: A:R.74, A:H.78, A:H.82 SO4.3: 5 residues within 4Å: Chain A: G.4, S.5, S.6, G.9, R.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.5, A:S.6 Salt bridges: A:R.13 SO4.4: 3 residues within 4Å: Chain A: G.4, Q.10, R.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.4, A:G.4, A:Q.10 Salt bridges: A:R.13 SO4.5: 3 residues within 4Å: Chain A: T.32, H.36 Ligands: LMT.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.36 SO4.9: 4 residues within 4Å: Chain A: D.20, N.23 Chain B: N.61 Ligands: LMT.7 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.23, B:I.60, B:N.61 SO4.11: 6 residues within 4Å: Chain B: Q.31, R.74, H.78, Q.81, H.82 Ligands: LMT.1 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.31, B:Q.81 Salt bridges: B:R.74, B:H.78, B:H.82 SO4.12: 3 residues within 4Å: Chain B: S.6, G.9, R.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.9 Salt bridges: B:R.13

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 4 residues within 4Å: Chain A: A.16, I.17, D.20, R.24 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.24, A:R.24 Salt bridges: A:R.24

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

EDO.13: 2 residues within 4Å: Chain B: R.24, R.25 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.24 Water bridges: B:R.25

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
C

B
D

Bcl-2 homologous antagonist/killer

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