SMTL ID : 8jol.1

cryo-EM structure of the CED-4/CED-3 holoenzyme

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.166, K.191, D.250 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.166 MG.3: 4 residues within 4Å: Chain B: S.166, K.191, D.250 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.166

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 19 residues within 4Å: Chain A: M.128, Y.131, R.160, G.162, S.163, G.164, K.165, S.166, V.167, R.273, F.301, Y.305, P.330, A.331, M.334, T.367, P.368, Y.369 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:Y.131, A:G.162, A:S.163, A:G.164, A:K.165, A:S.166, A:S.166, A:S.166, A:V.167, A:Y.305, A:T.367, A:T.367, A:P.368 Salt bridges: A:K.165, A:K.165, A:R.273 pi-Stacking: A:F.301 ATP.4: 19 residues within 4Å: Chain B: M.128, Y.131, A.161, G.162, S.163, G.164, K.165, S.166, V.167, R.273, F.301, Y.305, P.330, A.331, M.334, T.367, P.368, Y.369 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.162, B:G.164, B:K.165, B:S.166, B:S.166, B:V.167, B:Y.305, B:Y.305, B:T.367, B:T.367, B:P.368 Salt bridges: B:K.165, B:K.165, B:R.273 pi-Stacking: B:F.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Structural insights into CED-3 activation. Life Sci Alliance (2023)

Release Date

2023-06-28

Peptides

Cell death protein 4: AB
Cell death protein 3: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Cell death protein 4

Cell death protein 3

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