SMTL ID : 3jbt.1

Atomic structure of the Apaf-1 apoptosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-7-7-mer

Ligands

7 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 15 residues within 4Å: Chain A: V.125, F.126, V.127, C.158, G.159, K.160, S.161, V.162, D.244, R.265, I.294, P.321, S.325, Y.359 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.127, A:V.127, A:G.157, A:K.160, A:S.161, A:S.161, A:V.162, A:D.244, A:Y.359 Salt bridges: A:K.160, A:K.160, A:R.265 DTP.4: 15 residues within 4Å: Chain C: V.125, F.126, V.127, C.158, G.159, K.160, S.161, V.162, D.244, R.265, I.294, P.321, S.325, Y.359 Ligands: MG.5 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:V.127, C:V.127, C:G.157, C:K.160, C:S.161, C:S.161, C:V.162, C:D.244, C:Y.359 Salt bridges: C:K.160, C:K.160, C:R.265 DTP.7: 15 residues within 4Å: Chain E: V.125, F.126, V.127, C.158, G.159, K.160, S.161, V.162, D.244, R.265, I.294, P.321, S.325, Y.359 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:V.127, E:V.127, E:G.157, E:K.160, E:S.161, E:S.161, E:V.162, E:D.244, E:Y.359 Salt bridges: E:K.160, E:K.160, E:R.265 DTP.10: 15 residues within 4Å: Chain G: V.125, F.126, V.127, C.158, G.159, K.160, S.161, V.162, D.244, R.265, I.294, P.321, S.325, Y.359 Ligands: MG.11 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:V.127, G:V.127, G:G.157, G:K.160, G:S.161, G:S.161, G:V.162, G:D.244, G:Y.359 Salt bridges: G:K.160, G:K.160, G:R.265 DTP.13: 15 residues within 4Å: Chain I: V.125, F.126, V.127, C.158, G.159, K.160, S.161, V.162, D.244, R.265, I.294, P.321, S.325, Y.359 Ligands: MG.14 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:V.127, I:V.127, I:G.157, I:K.160, I:S.161, I:S.161, I:V.162, I:D.244, I:Y.359 Salt bridges: I:K.160, I:K.160, I:R.265 DTP.16: 15 residues within 4Å: Chain K: V.125, F.126, V.127, C.158, G.159, K.160, S.161, V.162, D.244, R.265, I.294, P.321, S.325, Y.359 Ligands: MG.17 12 PLIP interactions: 12 interactions with chain K Hydrogen bonds: K:V.127, K:V.127, K:G.157, K:K.160, K:S.161, K:S.161, K:V.162, K:D.244, K:Y.359 Salt bridges: K:K.160, K:K.160, K:R.265 DTP.19: 15 residues within 4Å: Chain M: V.125, F.126, V.127, C.158, G.159, K.160, S.161, V.162, D.244, R.265, I.294, P.321, S.325, Y.359 Ligands: MG.20 12 PLIP interactions: 12 interactions with chain M Hydrogen bonds: M:V.127, M:V.127, M:G.157, M:K.160, M:S.161, M:S.161, M:V.162, M:D.244, M:Y.359 Salt bridges: M:K.160, M:K.160, M:R.265

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.161, D.243 Ligands: DTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.161 MG.5: 3 residues within 4Å: Chain C: S.161, D.243 Ligands: DTP.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.161 MG.8: 3 residues within 4Å: Chain E: S.161, D.243 Ligands: DTP.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.161 MG.11: 3 residues within 4Å: Chain G: S.161, D.243 Ligands: DTP.10 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.161 MG.14: 3 residues within 4Å: Chain I: S.161, D.243 Ligands: DTP.13 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.161 MG.17: 3 residues within 4Å: Chain K: S.161, D.243 Ligands: DTP.16 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:S.161 MG.20: 3 residues within 4Å: Chain M: S.161, D.243 Ligands: DTP.19 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:S.161

7 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.3: 26 residues within 4Å: Chain B: K.14, C.15, C.18, H.19, T.29, G.30, P.31, L.33, L.36, R.39, T.41, G.42, F.47, Y.49, T.50, N.53, W.60, Y.68, L.69, T.79, K.80, M.81, I.82, F.83, L.95, L.99 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:T.29, B:L.33, B:L.33, B:L.36, B:F.47, B:W.60, B:Y.68, B:L.69, B:K.80, B:M.81, B:F.83, B:L.95, B:L.99 Hydrogen bonds: B:G.42, B:T.50, B:N.53, B:T.79, B:T.79, B:K.80 Salt bridges: B:R.39, B:K.80 Metal complexes: B:H.19 HEM.6: 26 residues within 4Å: Chain D: K.14, C.15, C.18, H.19, T.29, G.30, P.31, L.33, L.36, R.39, T.41, G.42, F.47, Y.49, T.50, N.53, W.60, Y.68, L.69, T.79, K.80, M.81, I.82, F.83, L.95, L.99 22 PLIP interactions: 22 interactions with chain D, Hydrophobic interactions: D:T.29, D:L.33, D:L.33, D:L.36, D:F.47, D:W.60, D:Y.68, D:L.69, D:K.80, D:M.81, D:F.83, D:L.95, D:L.99 Hydrogen bonds: D:G.42, D:T.50, D:N.53, D:T.79, D:T.79, D:K.80 Salt bridges: D:R.39, D:K.80 Metal complexes: D:H.19 HEM.9: 26 residues within 4Å: Chain F: K.14, C.15, C.18, H.19, T.29, G.30, P.31, L.33, L.36, R.39, T.41, G.42, F.47, Y.49, T.50, N.53, W.60, Y.68, L.69, T.79, K.80, M.81, I.82, F.83, L.95, L.99 22 PLIP interactions: 22 interactions with chain F, Hydrophobic interactions: F:T.29, F:L.33, F:L.33, F:L.36, F:F.47, F:W.60, F:Y.68, F:L.69, F:K.80, F:M.81, F:F.83, F:L.95, F:L.99 Hydrogen bonds: F:G.42, F:T.50, F:N.53, F:T.79, F:T.79, F:K.80 Salt bridges: F:R.39, F:K.80 Metal complexes: F:H.19 HEM.12: 26 residues within 4Å: Chain H: K.14, C.15, C.18, H.19, T.29, G.30, P.31, L.33, L.36, R.39, T.41, G.42, F.47, Y.49, T.50, N.53, W.60, Y.68, L.69, T.79, K.80, M.81, I.82, F.83, L.95, L.99 22 PLIP interactions: 22 interactions with chain H, Hydrophobic interactions: H:T.29, H:L.33, H:L.33, H:L.36, H:F.47, H:W.60, H:Y.68, H:L.69, H:K.80, H:M.81, H:F.83, H:L.95, H:L.99 Hydrogen bonds: H:G.42, H:T.50, H:N.53, H:T.79, H:T.79, H:K.80 Salt bridges: H:R.39, H:K.80 Metal complexes: H:H.19 HEM.15: 26 residues within 4Å: Chain J: K.14, C.15, C.18, H.19, T.29, G.30, P.31, L.33, L.36, R.39, T.41, G.42, F.47, Y.49, T.50, N.53, W.60, Y.68, L.69, T.79, K.80, M.81, I.82, F.83, L.95, L.99 22 PLIP interactions: 22 interactions with chain J, Hydrophobic interactions: J:T.29, J:L.33, J:L.33, J:L.36, J:F.47, J:W.60, J:Y.68, J:L.69, J:K.80, J:M.81, J:F.83, J:L.95, J:L.99 Hydrogen bonds: J:G.42, J:T.50, J:N.53, J:T.79, J:T.79, J:K.80 Salt bridges: J:R.39, J:K.80 Metal complexes: J:H.19 HEM.18: 26 residues within 4Å: Chain L: K.14, C.15, C.18, H.19, T.29, G.30, P.31, L.33, L.36, R.39, T.41, G.42, F.47, Y.49, T.50, N.53, W.60, Y.68, L.69, T.79, K.80, M.81, I.82, F.83, L.95, L.99 22 PLIP interactions: 22 interactions with chain L, Hydrophobic interactions: L:T.29, L:L.33, L:L.33, L:L.36, L:F.47, L:W.60, L:Y.68, L:L.69, L:K.80, L:M.81, L:F.83, L:L.95, L:L.99 Hydrogen bonds: L:G.42, L:T.50, L:N.53, L:T.79, L:T.79, L:K.80 Salt bridges: L:R.39, L:K.80 Metal complexes: L:H.19 HEM.21: 26 residues within 4Å: Chain N: K.14, C.15, C.18, H.19, T.29, G.30, P.31, L.33, L.36, R.39, T.41, G.42, F.47, Y.49, T.50, N.53, W.60, Y.68, L.69, T.79, K.80, M.81, I.82, F.83, L.95, L.99 22 PLIP interactions: 22 interactions with chain N, Hydrophobic interactions: N:T.29, N:L.33, N:L.33, N:L.36, N:F.47, N:W.60, N:Y.68, N:L.69, N:K.80, N:M.81, N:F.83, N:L.95, N:L.99 Hydrogen bonds: N:G.42, N:T.50, N:N.53, N:T.79, N:T.79, N:K.80 Salt bridges: N:R.39, N:K.80 Metal complexes: N:H.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, M. et al., Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1. Genes Dev. (2015)

Release Date

2015-11-18

Peptides

Apoptotic protease-activating factor 1: ACEGIKM
Cytochrome c: BDFHJLN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

M
M

B
B

D
D

F
F

H
H

J
J

L
L

N
N

Apoptotic protease-activating factor 1

Cytochrome c

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