SMTL ID : 8jns.1

cryo-EM structure of a CED-4 hexamer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-9-mer

Ligands

6 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 MG.5: 4 residues within 4Å: Chain C: S.166, K.191, D.250 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.166 MG.7: 4 residues within 4Å: Chain D: S.166, K.191, D.250 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.166 MG.9: 4 residues within 4Å: Chain E: S.166, K.191, D.250 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.166 MG.11: 4 residues within 4Å: Chain F: S.166, K.191, D.250 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.166

6 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, 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.3 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Y.131, B:G.162, B:S.163, B:G.164, B:K.165, B:S.166, B:S.166, B:S.166, B:V.167, 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 ATP.6: 20 residues within 4Å: Chain C: M.128, Y.131, R.160, G.162, S.163, G.164, K.165, S.166, V.167, Q.171, R.273, F.301, Y.305, P.330, A.331, M.334, T.367, P.368, Y.369 Ligands: MG.5 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:Y.131, C:G.162, C:G.164, C:K.165, C:S.166, C:S.166, C:S.166, C:V.167, C:Q.171, C:Y.305, C:T.367, C:T.367, C:P.368 Salt bridges: C:K.165, C:K.165, C:R.273 pi-Stacking: C:F.301 ATP.8: 19 residues within 4Å: Chain D: 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.7 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Y.131, D:G.162, D:S.163, D:G.164, D:K.165, D:S.166, D:S.166, D:S.166, D:V.167, D:Y.305, D:T.367, D:T.367, D:P.368 Salt bridges: D:K.165, D:K.165, D:R.273 pi-Stacking: D:F.301 ATP.10: 20 residues within 4Å: Chain E: M.128, Y.131, R.160, 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.9 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:Y.131, E:G.162, E:G.164, E:K.165, E:S.166, E:S.166, E:S.166, E:V.167, E:Q.171, E:Y.305, E:T.367, E:T.367, E:P.368 Salt bridges: E:K.165, E:K.165, E:R.273 pi-Stacking: E:F.301 ATP.12: 20 residues within 4Å: Chain F: M.128, Y.131, R.160, 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.11 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:Y.131, F:G.162, F:G.164, F:K.165, F:S.166, F:S.166, F:S.166, F:V.167, F:Y.305, F:T.367, F:T.367, F:P.368 Salt bridges: F:K.165, F:K.165, F:R.273 pi-Stacking: F: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: ABCDEFGHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

Cell death protein 4

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