SMTL ID : 4m9z.1

Crystal structure of CED-4 bound CED-3 fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.41 Å

Oligo State

homo-16-mer

Ligands

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

MSE-PHE-ASN-PHE-LEU-GLY.1: 8 residues within 4Å: Chain A: Q.379, V.382, E.383, R.390, A.394, V.467, V.468, D.469 9 PLIP interactions: 9 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, A:D.469 MSE-PHE-ASN-PHE-LEU-GLY.2: 10 residues within 4Å: Chain B: Q.379, V.382, E.383, R.390, S.391, A.394, H.466, V.467, V.468, D.469 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.382, B:V.382, B:R.390, B:A.394, B:V.467, B:V.468, B:D.469 Hydrogen bonds: B:V.467 MSE-PHE-ASN-PHE-LEU-GLY.3: 10 residues within 4Å: Chain C: Q.379, V.382, E.383, R.390, S.391, A.394, V.467, V.468, D.469, T.472 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-LEU-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 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.382, D:R.390, D:A.394, D:V.467, D:V.468 Hydrogen bonds: D:V.467, D:D.469 MSE-PHE-ASN-PHE-LEU-GLY.13: 8 residues within 4Å: Chain E: Q.379, V.382, E.383, R.390, A.394, V.467, V.468, D.469 9 PLIP interactions: 9 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, E:D.469 MSE-PHE-ASN-PHE-LEU-GLY.14: 10 residues within 4Å: Chain F: Q.379, V.382, E.383, R.390, S.391, A.394, H.466, V.467, V.468, D.469 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:V.382, F:V.382, F:R.390, F:A.394, F:V.467, F:V.468, F:D.469 Hydrogen bonds: F:V.467 MSE-PHE-ASN-PHE-LEU-GLY.15: 10 residues within 4Å: Chain G: Q.379, V.382, E.383, R.390, S.391, A.394, V.467, V.468, D.469, T.472 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:V.467, G:D.469 MSE-PHE-ASN-PHE-LEU-GLY.16: 9 residues within 4Å: Chain H: Q.379, V.382, E.383, R.390, A.394, V.467, V.468, D.469, T.472 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:V.382, H:R.390, H:A.394, H:V.467, H:V.468 Hydrogen bonds: H:V.467, H:D.469 MSE-PHE-ASN-PHE-LEU-GLY.25: 8 residues within 4Å: Chain I: Q.379, V.382, E.383, R.390, A.394, V.467, V.468, D.469 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:V.382, I:E.383, I:R.390, I:A.394, I:V.467, I:V.468 Hydrogen bonds: I:Q.379, I:V.467, I:D.469 MSE-PHE-ASN-PHE-LEU-GLY.26: 10 residues within 4Å: Chain J: Q.379, V.382, E.383, R.390, S.391, A.394, H.466, V.467, V.468, D.469 8 PLIP interactions: 8 interactions with chain J Hydrophobic interactions: J:V.382, J:V.382, J:R.390, J:A.394, J:V.467, J:V.468, J:D.469 Hydrogen bonds: J:V.467 MSE-PHE-ASN-PHE-LEU-GLY.27: 10 residues within 4Å: Chain K: Q.379, V.382, E.383, R.390, S.391, A.394, V.467, V.468, D.469, T.472 8 PLIP interactions: 8 interactions with chain K Hydrophobic interactions: K:V.382, K:E.383, K:R.390, K:A.394, K:V.467, K:V.468 Hydrogen bonds: K:V.467, K:D.469 MSE-PHE-ASN-PHE-LEU-GLY.28: 9 residues within 4Å: Chain L: Q.379, V.382, E.383, R.390, A.394, V.467, V.468, D.469, T.472 7 PLIP interactions: 7 interactions with chain L Hydrophobic interactions: L:V.382, L:R.390, L:A.394, L:V.467, L:V.468 Hydrogen bonds: L:V.467, L:D.469 MSE-PHE-ASN-PHE-LEU-GLY.37: 8 residues within 4Å: Chain M: Q.379, V.382, E.383, R.390, A.394, V.467, V.468, D.469 9 PLIP interactions: 9 interactions with chain M Hydrophobic interactions: M:V.382, M:E.383, M:R.390, M:A.394, M:V.467, M:V.468 Hydrogen bonds: M:Q.379, M:V.467, M:D.469 MSE-PHE-ASN-PHE-LEU-GLY.38: 10 residues within 4Å: Chain N: Q.379, V.382, E.383, R.390, S.391, A.394, H.466, V.467, V.468, D.469 8 PLIP interactions: 8 interactions with chain N Hydrophobic interactions: N:V.382, N:V.382, N:R.390, N:A.394, N:V.467, N:V.468, N:D.469 Hydrogen bonds: N:V.467 MSE-PHE-ASN-PHE-LEU-GLY.39: 10 residues within 4Å: Chain O: Q.379, V.382, E.383, R.390, S.391, A.394, V.467, V.468, D.469, T.472 8 PLIP interactions: 8 interactions with chain O Hydrophobic interactions: O:V.382, O:E.383, O:R.390, O:A.394, O:V.467, O:V.468 Hydrogen bonds: O:V.467, O:D.469 MSE-PHE-ASN-PHE-LEU-GLY.40: 9 residues within 4Å: Chain P: Q.379, V.382, E.383, R.390, A.394, V.467, V.468, D.469, T.472 7 PLIP interactions: 7 interactions with chain P Hydrophobic interactions: P:V.382, P:R.390, P:A.394, P:V.467, P:V.468 Hydrogen bonds: P:V.467, P:D.469

16 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: S.166, D.250, D.251, 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 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.166 MG.9: 4 residues within 4Å: Chain C: S.166, K.191, D.250 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.166 MG.11: 6 residues within 4Å: Chain D: K.165, 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.17: 5 residues within 4Å: Chain E: S.166, D.250, D.251, T.271 Ligands: ATP.18 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:S.166, E:D.250 MG.19: 3 residues within 4Å: Chain F: S.166, D.250 Ligands: ATP.20 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.166 MG.21: 4 residues within 4Å: Chain G: S.166, K.191, D.250 Ligands: ATP.22 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.166 MG.23: 6 residues within 4Å: Chain H: K.165, 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 MG.29: 5 residues within 4Å: Chain I: S.166, D.250, D.251, T.271 Ligands: ATP.30 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:S.166, I:D.250 MG.31: 3 residues within 4Å: Chain J: S.166, D.250 Ligands: ATP.32 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.166 MG.33: 4 residues within 4Å: Chain K: S.166, K.191, D.250 Ligands: ATP.34 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:S.166 MG.35: 6 residues within 4Å: Chain L: K.165, S.166, D.250, D.251, T.271 Ligands: ATP.36 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:S.166, L:D.250 MG.41: 5 residues within 4Å: Chain M: S.166, D.250, D.251, T.271 Ligands: ATP.42 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:S.166, M:D.250 MG.43: 3 residues within 4Å: Chain N: S.166, D.250 Ligands: ATP.44 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:S.166 MG.45: 4 residues within 4Å: Chain O: S.166, K.191, D.250 Ligands: ATP.46 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:S.166 MG.47: 6 residues within 4Å: Chain P: K.165, S.166, D.250, D.251, T.271 Ligands: ATP.48 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:S.166, P:D.250

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

ATP.6: 20 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, R.273, F.301, Y.305, P.330, A.331, M.334, T.367, P.368, Y.369 Ligands: MG.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.131, 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 12 PLIP interactions: 12 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:Y.305, B:Y.369 Salt bridges: B:K.165, B:K.165, B:R.273 pi-Stacking: 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 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Y.131, C:G.162, C:G.164, C:K.165, 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: 18 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, 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.369, D:Y.369 Salt bridges: D:K.165, D:K.165, D:R.273 pi-Stacking: D:F.301 ATP.18: 20 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, R.273, F.301, Y.305, P.330, A.331, M.334, T.367, P.368, Y.369 Ligands: MG.17 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:Y.131, E:G.162, E:G.164, E:K.165, E:S.166, E:V.167, E:Y.305, E:Y.369 Salt bridges: E:K.165, E:K.165, E:R.273 pi-Stacking: E:F.301 ATP.20: 18 residues within 4Å: Chain F: 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.19 12 PLIP interactions: 12 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:Y.305, F:Y.369 Salt bridges: F:K.165, F:K.165, F:R.273 pi-Stacking: F:F.301 ATP.22: 20 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, 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:G.164, G:K.165, G:S.166, G:V.167, G:Q.171, G:Y.369, G:Y.369 Salt bridges: G:K.165, G:K.165, G:R.273 pi-Stacking: G:F.301 ATP.24: 18 residues within 4Å: Chain H: M.128, Y.131, A.161, G.162, G.164, K.165, S.166, V.167, Q.171, R.273, F.301, 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.369, H:Y.369 Salt bridges: H:K.165, H:K.165, H:R.273 pi-Stacking: H:F.301 ATP.30: 20 residues within 4Å: Chain I: 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.29 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:Y.131, I:G.162, I:G.164, I:K.165, I:S.166, I:V.167, I:Y.305, I:Y.369 Salt bridges: I:K.165, I:K.165, I:R.273 pi-Stacking: I:F.301 ATP.32: 18 residues within 4Å: Chain J: 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.31 12 PLIP interactions: 12 interactions with chain J Hydrogen bonds: J:Y.131, J:G.162, J:G.164, J:K.165, J:S.166, J:V.167, J:Y.305, J:Y.369 Salt bridges: J:K.165, J:K.165, J:R.273 pi-Stacking: J:F.301 ATP.34: 20 residues within 4Å: Chain K: 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.33 13 PLIP interactions: 13 interactions with chain K Hydrogen bonds: K:Y.131, K:G.162, K:G.164, K:K.165, K:S.166, K:V.167, K:Q.171, K:Y.369, K:Y.369 Salt bridges: K:K.165, K:K.165, K:R.273 pi-Stacking: K:F.301 ATP.36: 18 residues within 4Å: Chain L: M.128, Y.131, A.161, G.162, G.164, K.165, S.166, V.167, Q.171, R.273, F.301, P.330, A.331, M.334, T.367, P.368, Y.369 Ligands: MG.35 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:Y.131, L:G.162, L:G.164, L:K.165, L:S.166, L:V.167, L:Q.171, L:Y.369, L:Y.369 Salt bridges: L:K.165, L:K.165, L:R.273 pi-Stacking: L:F.301 ATP.42: 20 residues within 4Å: Chain M: 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.41 12 PLIP interactions: 12 interactions with chain M Hydrogen bonds: M:Y.131, M:G.162, M:G.164, M:K.165, M:S.166, M:V.167, M:Y.305, M:Y.369 Salt bridges: M:K.165, M:K.165, M:R.273 pi-Stacking: M:F.301 ATP.44: 18 residues within 4Å: Chain N: 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.43 12 PLIP interactions: 12 interactions with chain N Hydrogen bonds: N:Y.131, N:G.162, N:G.164, N:K.165, N:S.166, N:V.167, N:Y.305, N:Y.369 Salt bridges: N:K.165, N:K.165, N:R.273 pi-Stacking: N:F.301 ATP.46: 20 residues within 4Å: Chain O: 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.45 13 PLIP interactions: 13 interactions with chain O Hydrogen bonds: O:Y.131, O:G.162, O:G.164, O:K.165, O:S.166, O:V.167, O:Q.171, O:Y.369, O:Y.369 Salt bridges: O:K.165, O:K.165, O:R.273 pi-Stacking: O:F.301 ATP.48: 18 residues within 4Å: Chain P: M.128, Y.131, A.161, G.162, G.164, K.165, S.166, V.167, Q.171, R.273, F.301, P.330, A.331, M.334, T.367, P.368, Y.369 Ligands: MG.47 13 PLIP interactions: 13 interactions with chain P Hydrogen bonds: P:Y.131, P:G.162, P:G.164, P:K.165, P:S.166, P:V.167, P:Q.171, P:Y.369, P:Y.369 Salt bridges: P:K.165, P:K.165, P:R.273 pi-Stacking: P: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: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

M
A

N
B

O
C

P
D

Cell death protein 4

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