SMTL ID : 4m9s.1

crystal structure of CED-4 bound CED-3 fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.21 Å

Oligo State

homo-tetramer

Ligands

4 x MSE- PHE- ASN- PHE- MSE- GLY: CED-3 fragment(Non-covalent)

MSE-PHE-ASN-PHE-MSE-GLY.1: 9 residues within 4Å: Chain A: Q.379, V.382, E.383, R.390, S.391, A.394, V.467, V.468, D.469 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.382, A:E.383, A:R.390, A:A.394, A:V.467 Hydrogen bonds: A:Q.379, A:V.467, A:V.467, A:D.469, A:D.469 MSE-PHE-ASN-PHE-MSE-GLY.2: 11 residues within 4Å: Chain B: Q.379, V.382, E.383, R.390, S.391, A.394, F.463, H.466, V.467, V.468, D.469 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.382, B:E.383, B:R.390, B:A.394, B:V.467, B:V.468, B:D.469 Hydrogen bonds: B:V.467, B:D.469 MSE-PHE-ASN-PHE-MSE-GLY.3: 9 residues within 4Å: Chain C: Q.379, V.382, E.383, R.390, S.391, A.394, V.467, V.468, D.469 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.382, C:E.383, C:R.390, C:A.394, C:V.467, C:V.468 Hydrogen bonds: C:V.467, C:D.469 MSE-PHE-ASN-PHE-MSE-GLY.4: 9 residues within 4Å: Chain D: Q.379, V.382, E.383, R.390, A.394, V.467, V.468, D.469, T.472 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.382, D:R.390, D:A.394, D:V.467, D:V.468 Hydrogen bonds: D:Q.379, D:E.383, D:V.467

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: S.166, D.250, T.271 Ligands: ATP.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.166, A:D.250 MG.7: 3 residues within 4Å: Chain B: S.166, D.250 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.166, B:D.250 MG.9: 3 residues within 4Å: Chain C: S.166, K.191 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.166 MG.11: 4 residues within 4Å: Chain D: S.166, D.250, D.251 Ligands: ATP.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:S.166, D:D.250

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

ATP.6: 20 residues within 4Å: Chain A: M.128, Y.131, R.133, A.161, G.162, 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 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.131, A:R.133, A:G.162, A:G.164, A:K.165, A:S.166, A:V.167, A:Y.305, A:Y.369 Salt bridges: A:K.165, A:K.165, A:R.273 pi-Stacking: A:F.301 ATP.8: 18 residues within 4Å: Chain B: M.128, Y.131, A.161, G.162, 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 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.162, B:G.164, B:K.165, B:S.166, B:V.167, B:Y.305, B:Y.305, B:Y.369 Salt bridges: B:K.165, B:K.165, B:R.273 pi-Stacking: B:F.301, B:F.301 ATP.10: 20 residues within 4Å: Chain C: M.128, Y.131, A.161, 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 14 PLIP interactions: 14 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:V.167, C:Q.171, C:Y.369, C:Y.369 Salt bridges: C:K.165, C:K.165, C:R.273 pi-Stacking: C:F.301 ATP.12: 19 residues within 4Å: Chain D: M.128, Y.131, A.161, G.162, 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.11 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:Y.131, D:G.162, D:G.164, D:K.165, D:S.166, D:S.166, D:V.167, D:Q.171, D:Y.369, D:Y.369 Salt bridges: D:K.165, D:K.165, D:R.273 pi-Stacking: D:F.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, W. et al., Mechanistic insights into CED-4-mediated activation of CED-3. Genes Dev. (2013)

Release Date

2013-10-23

Peptides

Cell death protein 4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cell death protein 4

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