SMTL ID : 8jo0.1

The Cryo-EM structure of a heptameric CED-4/CED-3 catalytic complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-7-mer

Ligands

7 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain G: S.166, K.191, D.250 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.166 MG.3: 4 residues within 4Å: Chain H: S.166, K.191, D.250 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.166 MG.5: 4 residues within 4Å: Chain I: S.166, K.191, D.250 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.166 MG.7: 4 residues within 4Å: Chain J: S.166, K.191, D.250 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.166 MG.9: 4 residues within 4Å: Chain K: S.166, K.191, D.250 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:S.166 MG.11: 4 residues within 4Å: Chain L: S.166, K.191, D.250 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:S.166 MG.13: 4 residues within 4Å: Chain M: S.166, K.191, D.250 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:S.166

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

ATP.2: 18 residues within 4Å: Chain G: 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, P.368, Y.369 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:Y.131, G:G.162, G:S.163, G:G.164, G:K.165, G:S.166, G:S.166, G:S.166, G:V.167, G:Y.305, G:Y.369 Salt bridges: G:K.165, G:K.165, G:R.273 pi-Stacking: G:F.301 ATP.4: 19 residues within 4Å: Chain H: M.128, Y.131, 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.3 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:Y.131, H:G.162, H:S.163, H:G.164, H:K.165, H:S.166, H:S.166, H:S.166, H:V.167, H:Q.171, H:T.367, H:T.367, H:P.368 Salt bridges: H:K.165, H:K.165, H:R.273 pi-Stacking: H:F.301 ATP.6: 17 residues within 4Å: Chain I: M.128, Y.131, G.162, S.163, G.164, K.165, S.166, V.167, R.273, Y.305, P.330, A.331, M.334, T.367, P.368, Y.369 Ligands: MG.5 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:Y.131, I:G.162, I:S.163, I:G.164, I:K.165, I:S.166, I:S.166, I:S.166, I:V.167, I:T.367, I:T.367, I:P.368 Salt bridges: I:K.165, I:K.165, I:R.273 ATP.8: 18 residues within 4Å: Chain J: M.128, Y.131, 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 16 PLIP interactions: 16 interactions with chain J Hydrogen bonds: J:Y.131, J:G.162, J:S.163, J:G.164, J:K.165, J:S.166, J:S.166, J:S.166, J:V.167, J:Y.305, J:T.367, J:Y.369 Salt bridges: J:K.165, J:K.165, J:R.273 pi-Stacking: J:F.301 ATP.10: 19 residues within 4Å: Chain K: M.128, Y.131, 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.9 18 PLIP interactions: 18 interactions with chain K Hydrogen bonds: K:Y.131, K:G.162, K:S.163, K:G.164, K:K.165, K:S.166, K:S.166, K:S.166, K:V.167, K:Q.171, K:Y.305, K:T.367, K:T.367, K:P.368 Salt bridges: K:K.165, K:K.165, K:R.273 pi-Stacking: K:F.301 ATP.12: 19 residues within 4Å: Chain L: 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.11 16 PLIP interactions: 16 interactions with chain L Hydrogen bonds: L:Y.131, L:G.162, L:S.163, L:G.164, L:K.165, L:S.166, L:S.166, L:S.166, L:V.167, L:T.367, L:T.367, L:P.368 Salt bridges: L:K.165, L:K.165, L:R.273 pi-Stacking: L:F.301 ATP.14: 19 residues within 4Å: Chain M: 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.13 16 PLIP interactions: 16 interactions with chain M Hydrogen bonds: M:Y.131, M:G.162, M:S.163, M:G.164, M:K.165, M:S.166, M:S.166, M:S.166, M:V.167, M:T.367, M:T.367, M:Y.369 Salt bridges: M:K.165, M:K.165, M:R.273 pi-Stacking: M: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: ABCDEF
Cell death protein 4: GHIJKLM

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
J

D
K

E
L

F
M

G
A

H
B

I
C

J
D

K
E

L
F

M
G

Cell death protein 4

Cell death protein 4

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