SMTL ID : 8uky.2 (1 other biounit)

Crystal structure of BAK in complex with inhibiting antibody 14G6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-1-mer

Ligands

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 10 residues within 4Å: Chain A: P.118, P.119, L.124, Y.185, F.208, N.209, R.210, G.211, E.212 Chain B: S.132 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.132, B:S.132, A:D.121, A:Y.185, A:G.211 PEG.6: 11 residues within 4Å: Chain A: Q.159, E.160, S.161, S.175, S.176, T.177 Chain B: L.146, V.174, S.182, L.183, S.184 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.161, A:S.175, A:T.177, B:S.184 Water bridges: A:S.175, B:S.184 PEG.8: 5 residues within 4Å: Chain B: T.58, N.59, Y.60, K.65 Ligands: PEG.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.59, B:Y.60 PEG.9: 5 residues within 4Å: Chain B: G.56, G.57, T.58 Chain C: L.131 Ligands: PEG.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.56, B:T.58 PEG.12: 3 residues within 4Å: Chain C: N.108, W.109, G.110 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.109, C:G.110 Water bridges: C:N.108, C:N.108

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

EDO.2: 4 residues within 4Å: Chain A: D.166, D.169 Chain B: G.167, H.169 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.167 Water bridges: A:D.169 EDO.4: 6 residues within 4Å: Chain A: S.43, K.45 Chain B: L.4, W.108, G.109, Q.110 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.43, A:S.43, A:K.45 Water bridges: B:L.4

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 13 residues within 4Å: Chain A: Q.38, K.39, P.40, G.41, Q.42, D.85 Chain B: A.9, V.93, F.95, Q.110, G.111, T.112, T.113 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.41, A:D.85, B:T.113 Water bridges: B:Q.110

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

SO4.5: 5 residues within 4Å: Chain A: T.31, W.50, S.52, T.53 Chain C: E.16 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.52, A:S.52, C:E.16 SO4.11: 2 residues within 4Å: Chain B: Q.43, G.44 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.43, B:G.44 Water bridges: B:L.45

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 10 residues within 4Å: Chain A: N.137, T.163, E.164, D.166, T.171, Y.172, S.173 Chain B: V.168, H.169, T.170 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.163, A:T.171, A:Y.172, B:T.170, B:T.170 Water bridges: B:T.170

1 x 144: TRIS-HYDROXYMETHYL-METHYL-AMMONIUM(Non-covalent)

144.10: 9 residues within 4Å: Chain B: Y.150, E.153, P.154, V.155, T.170, F.171, P.172, A.173, L.183 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.155, B:T.170 Salt bridges: B:E.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Subas Satish, H.P. et al., A novel inhibitory BAK antibody enables assessment of non-activated BAK in cancer cells. Cell Death Differ. (2024)

Release Date

2024-04-10

Peptides

14G6 Fab light chain: A
14G6 Fab heavy chain: B
Bcl-2 homologous antagonist/killer: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

14G6 Fab light chain

14G6 Fab heavy chain

Bcl-2 homologous antagonist/killer

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