SMTL ID : 5vwv.2 (1 other biounit)

Bak core latch dimer in complex with Bim-BH3 - Cubic

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-mer

Ligands

2 x TFA: trifluoroacetic acid(Non-covalent)

TFA.1: 10 residues within 4Å: Chain A: Y.22, R.26, N.70, Y.73, F.77, A.114, G.117, R.121 Chain B: L.12, I.15 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.70 Salt bridges: A:R.26, A:R.121 TFA.10: 10 residues within 4Å: Chain C: Y.22, R.26, N.70, Y.73, F.77, A.114, G.117, R.121 Chain D: L.12, I.15 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.22 Water bridges: C:N.70 Salt bridges: C:R.26, C:R.121

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

EDO.2: 4 residues within 4Å: Chain A: E.76, M.80 Chain B: R.7, E.11 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.76, B:R.7 Water bridges: A:T.79, A:T.79 EDO.3: 2 residues within 4Å: Chain A: A.88, E.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.88 Water bridges: A:Q.137, A:Q.137 EDO.4: 5 residues within 4Å: Chain A: S.105, G.106, I.107, N.108, R.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.107, A:N.108 Water bridges: A:I.107 EDO.5: 5 residues within 4Å: Chain A: Y.25, Q.28, E.32, R.60 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.32 EDO.6: 6 residues within 4Å: Chain A: F.24, Y.25, Q.28, L.47, P.51 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.28 EDO.9: 7 residues within 4Å: Chain A: W.109 Chain B: Y.23, A.24, R.25 Chain C: A.163, N.166, L.167 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:W.109 Hydrogen bonds: B:Y.23 EDO.11: 4 residues within 4Å: Chain C: E.76, M.80 Chain D: R.7, E.11 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.76, C:E.76, D:R.7 Water bridges: C:T.79 EDO.12: 2 residues within 4Å: Chain C: A.88, E.89 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.88 Water bridges: C:Q.137, C:Q.137 EDO.13: 5 residues within 4Å: Chain C: S.105, G.106, I.107, N.108, R.111 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.107, C:N.108 Water bridges: C:I.107 EDO.14: 5 residues within 4Å: Chain C: Y.25, Q.28, E.32, R.60 Ligands: EDO.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.32 EDO.15: 6 residues within 4Å: Chain C: F.24, Y.25, Q.28, L.47, P.51 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.28 EDO.18: 7 residues within 4Å: Chain A: A.163, N.166, L.167 Chain C: W.109 Chain D: Y.23, A.24, R.25 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:W.109 Hydrogen bonds: D:Y.23

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: M.80, H.83 Chain B: P.4, R.7 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain C: M.80, H.83 Chain D: P.4, R.7 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: F.77, Q.78, L.81, R.121, L.124, H.125, Q.128 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.121, A:H.125 Water bridges: A:Q.128 GOL.17: 7 residues within 4Å: Chain C: F.77, Q.78, L.81, R.121, L.124, H.125, Q.128 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.121, C:H.125 Water bridges: C:Q.78, C:Q.128, C:H.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brouwer, J.M. et al., Conversion of Bim-BH3 from Activator to Inhibitor of Bak through Structure-Based Design. Mol. Cell (2017)

Release Date

2017-11-15

Peptides

Bcl-2 homologous antagonist/killer: AC
Bcl-2-like protein 11: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Bcl-2 homologous antagonist/killer

Bcl-2-like protein 11

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