SMTL ID : 4m9y.1

Crystal structure of CED-4 bound CED-3 fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.20 Å

Oligo State

homo-octamer

Ligands

8 x PRO- LEU- PHE- ASN- PHE- MSE- GLY: CED-3 fragment(Non-covalent)

PRO-LEU-PHE-ASN-PHE-MSE-GLY.1: 8 residues within 4Å: Chain A: Q.379, V.382, E.383, R.390, A.394, V.467, V.468, D.469 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.382, A:E.383, A:R.390, A:A.394, A:V.467, A:V.468 Hydrogen bonds: A:Q.379, A:V.467 PRO-LEU-PHE-ASN-PHE-MSE-GLY.2: 9 residues within 4Å: Chain B: Q.379, V.382, E.383, R.390, A.394, F.463, H.466, V.467, V.468 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.382, B:E.383, B:R.390, B:A.394, B:V.467, B:V.468 Hydrogen bonds: B:Q.379, B:V.467 PRO-LEU-PHE-ASN-PHE-MSE-GLY.7: 8 residues within 4Å: Chain C: Q.379, V.382, E.383, R.390, 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:Q.379, C:V.467 PRO-LEU-PHE-ASN-PHE-MSE-GLY.8: 9 residues within 4Å: Chain D: Q.379, V.382, E.383, R.390, A.394, F.463, H.466, V.467, V.468 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.382, D:E.383, D:R.390, D:A.394, D:V.467, D:V.468 Hydrogen bonds: D:Q.379, D:V.467 PRO-LEU-PHE-ASN-PHE-MSE-GLY.13: 8 residues within 4Å: Chain E: Q.379, V.382, E.383, R.390, A.394, V.467, V.468, D.469 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:V.382, E:E.383, E:R.390, E:A.394, E:V.467, E:V.468 Hydrogen bonds: E:Q.379, E:V.467 PRO-LEU-PHE-ASN-PHE-MSE-GLY.14: 9 residues within 4Å: Chain F: Q.379, V.382, E.383, R.390, A.394, F.463, H.466, V.467, V.468 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:V.382, F:E.383, F:R.390, F:A.394, F:V.467, F:V.468 Hydrogen bonds: F:Q.379, F:V.467 PRO-LEU-PHE-ASN-PHE-MSE-GLY.19: 8 residues within 4Å: Chain G: Q.379, V.382, E.383, R.390, A.394, V.467, V.468, D.469 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:V.382, G:E.383, G:R.390, G:A.394, G:V.467, G:V.468 Hydrogen bonds: G:Q.379, G:V.467 PRO-LEU-PHE-ASN-PHE-MSE-GLY.20: 9 residues within 4Å: Chain H: Q.379, V.382, E.383, R.390, A.394, F.463, H.466, V.467, V.468 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:V.382, H:E.383, H:R.390, H:A.394, H:V.467, H:V.468 Hydrogen bonds: H:Q.379, H:V.467

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: S.166, K.191, D.250, D.251 Ligands: ATP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.166, A:D.250 MG.5: 5 residues within 4Å: Chain B: S.166, D.250, D.251, T.271 Ligands: ATP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.166, B:D.250 MG.9: 5 residues within 4Å: Chain C: S.166, K.191, D.250, D.251 Ligands: ATP.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.166, C:D.250 MG.11: 5 residues within 4Å: Chain D: S.166, D.250, D.251, T.271 Ligands: ATP.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:S.166, D:D.250 MG.15: 5 residues within 4Å: Chain E: S.166, K.191, D.250, D.251 Ligands: ATP.16 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:S.166, E:D.250 MG.17: 5 residues within 4Å: Chain F: S.166, D.250, D.251, T.271 Ligands: ATP.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:S.166, F:D.250 MG.21: 5 residues within 4Å: Chain G: S.166, K.191, D.250, D.251 Ligands: ATP.22 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:S.166, G:D.250 MG.23: 5 residues within 4Å: Chain H: S.166, D.250, D.251, T.271 Ligands: ATP.24 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:S.166, H:D.250

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

ATP.4: 21 residues within 4Å: Chain A: M.128, Y.131, A.161, G.162, S.163, G.164, K.165, S.166, V.167, Q.171, D.251, R.273, F.301, Y.305, P.330, A.331, M.334, T.367, P.368, Y.369 Ligands: MG.3 13 PLIP interactions: 13 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:V.167, A:Q.171, A:Y.305, A:Y.369 Salt bridges: A:K.165, A:K.165, A:R.273 ATP.6: 21 residues within 4Å: Chain B: M.128, Y.131, A.161, G.162, S.163, G.164, K.165, S.166, V.167, Q.171, D.251, 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 B Hydrogen bonds: B:Y.131, B:G.162, B:G.164, B:K.165, B:S.166, B:V.167, B:Q.171, B:Y.305, B:Y.369 Salt bridges: B:K.165, B:K.165, B:R.273 pi-Stacking: B:F.301 ATP.10: 21 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, D.251, R.273, F.301, Y.305, P.330, A.331, M.334, T.367, P.368, Y.369 Ligands: MG.9 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Y.131, C:G.162, C:S.163, C:G.164, C:K.165, C:S.166, C:V.167, C:Q.171, C:Y.305, C:Y.369 Salt bridges: C:K.165, C:K.165, C:R.273 ATP.12: 21 residues within 4Å: Chain D: M.128, Y.131, A.161, G.162, S.163, G.164, K.165, S.166, V.167, Q.171, D.251, R.273, F.301, Y.305, P.330, A.331, M.334, T.367, P.368, Y.369 Ligands: MG.11 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Y.131, D:G.162, D:G.164, D:K.165, D:S.166, D:V.167, D:Q.171, D:Y.305, D:Y.369 Salt bridges: D:K.165, D:K.165, D:R.273 pi-Stacking: D:F.301 ATP.16: 21 residues within 4Å: Chain E: M.128, Y.131, A.161, G.162, S.163, G.164, K.165, S.166, V.167, Q.171, D.251, R.273, F.301, Y.305, P.330, A.331, M.334, T.367, P.368, Y.369 Ligands: MG.15 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:Y.131, E:G.162, E:S.163, E:G.164, E:K.165, E:S.166, E:V.167, E:Q.171, E:Y.305, E:Y.369 Salt bridges: E:K.165, E:K.165, E:R.273 ATP.18: 21 residues within 4Å: Chain F: M.128, Y.131, A.161, G.162, S.163, G.164, K.165, S.166, V.167, Q.171, D.251, R.273, F.301, Y.305, P.330, A.331, M.334, T.367, P.368, Y.369 Ligands: MG.17 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:Y.131, F:G.162, F:G.164, F:K.165, F:S.166, F:V.167, F:Q.171, F:Y.305, F:Y.369 Salt bridges: F:K.165, F:K.165, F:R.273 pi-Stacking: F:F.301 ATP.22: 21 residues within 4Å: Chain G: M.128, Y.131, A.161, G.162, S.163, G.164, K.165, S.166, V.167, Q.171, D.251, R.273, F.301, Y.305, P.330, A.331, M.334, T.367, P.368, Y.369 Ligands: MG.21 13 PLIP interactions: 13 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:V.167, G:Q.171, G:Y.305, G:Y.369 Salt bridges: G:K.165, G:K.165, G:R.273 ATP.24: 21 residues within 4Å: Chain H: M.128, Y.131, A.161, G.162, S.163, G.164, K.165, S.166, V.167, Q.171, D.251, R.273, F.301, Y.305, P.330, A.331, M.334, T.367, P.368, Y.369 Ligands: MG.23 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:Y.131, H:G.162, H:G.164, H:K.165, H:S.166, H:V.167, H:Q.171, H:Y.305, H:Y.369 Salt bridges: H:K.165, H:K.165, H:R.273 pi-Stacking: H: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: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Cell death protein 4

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