SMTL ID : 6uxo.4 (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

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

SO4.1: 4 residues within 4Å: Chain A: Q.31, R.74, H.78, H.82 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.82 Salt bridges: A:R.74, A:H.78, A:H.82 SO4.2: 5 residues within 4Å: Chain A: G.4, S.5, S.6, G.9, R.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.4, A:S.5, A:S.6, A:G.9 Salt bridges: A:R.13 SO4.3: 3 residues within 4Å: Chain A: G.4, Q.10, R.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.4, A:Q.10 Salt bridges: A:R.13 SO4.4: 3 residues within 4Å: Chain A: T.32, H.36 Ligands: LMT.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.36 SO4.11: 2 residues within 4Å: Chain A: R.25 Chain B: R.25 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:R.25 Salt bridges: B:R.25 Hydrogen bonds: A:R.25 SO4.13: 4 residues within 4Å: Chain B: Q.31, R.74, H.78, H.82 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.31, B:Q.31 Salt bridges: B:R.74, B:H.78, B:H.82 SO4.14: 3 residues within 4Å: Chain B: S.6, G.9, R.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.6, B:S.6, B:G.9 Salt bridges: B:R.13

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

ACT.5: 3 residues within 4Å: Chain A: I.17, D.20, R.24 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.20 Water bridges: A:R.24, A:R.24 Salt bridges: A:R.24

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

LMT.6: 11 residues within 4Å: Chain A: N.23, D.27, Q.31, L.69, Y.73, R.74, L.77 Chain B: I.60, N.61, W.62, L.69 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.73, A:Y.73, A:Y.73, B:W.62, B:L.69 Hydrogen bonds: A:N.23, A:N.23, A:Q.31, A:R.74, A:R.74, B:I.60, B:I.60 Water bridges: B:I.60, B:W.62 LMT.7: 3 residues within 4Å: Chain A: Q.35, H.36 Ligands: SO4.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.35 Salt bridges: A:H.36 LMT.10: 9 residues within 4Å: Chain A: I.60, N.61, W.62, V.65 Chain B: N.23, D.27, Y.73, R.74 Ligands: LMT.12 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.73, B:Y.73, A:W.62, A:V.65, A:V.65 Hydrogen bonds: B:N.23, B:D.27, A:W.62 Water bridges: B:N.23 LMT.12: 9 residues within 4Å: Chain B: A.41, E.42, A.44, Y.45, F.48, L.69, G.72, A.76 Ligands: LMT.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.44, B:F.48, B:F.48, B:L.69, B:A.76 Hydrogen bonds: B:E.42 Water bridges: B:Y.45

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

EDO.8: 5 residues within 4Å: Chain A: S.58, R.64 Chain B: R.13, A.16, D.20 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.58, A:R.64, B:D.20 EDO.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.15: 2 residues within 4Å: Chain B: T.32, Q.35 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.32, B:Q.35

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
G

B
H

Bcl-2 homologous antagonist/killer

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