SMTL ID : 4v4l.1

Structure of the Drosophila apoptosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-16-mer

Ligands

16 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.164, L.251 Ligands: DTP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.164 MG.3: 3 residues within 4Å: Chain B: T.164, L.251 Ligands: DTP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.164 MG.5: 3 residues within 4Å: Chain C: T.164, L.251 Ligands: DTP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.164 MG.7: 3 residues within 4Å: Chain D: T.164, L.251 Ligands: DTP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.164 MG.9: 3 residues within 4Å: Chain E: T.164, L.251 Ligands: DTP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.164 MG.11: 3 residues within 4Å: Chain F: T.164, L.251 Ligands: DTP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.164 MG.13: 3 residues within 4Å: Chain G: T.164, L.251 Ligands: DTP.14 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.164 MG.15: 3 residues within 4Å: Chain H: T.164, L.251 Ligands: DTP.16 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.164 MG.17: 3 residues within 4Å: Chain I: T.164, L.251 Ligands: DTP.18 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.164 MG.19: 3 residues within 4Å: Chain J: T.164, L.251 Ligands: DTP.20 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.164 MG.21: 3 residues within 4Å: Chain K: T.164, L.251 Ligands: DTP.22 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.164 MG.23: 3 residues within 4Å: Chain L: T.164, L.251 Ligands: DTP.24 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.164 MG.25: 3 residues within 4Å: Chain M: T.164, L.251 Ligands: DTP.26 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.164 MG.27: 3 residues within 4Å: Chain N: T.164, L.251 Ligands: DTP.28 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:T.164 MG.29: 3 residues within 4Å: Chain O: T.164, L.251 Ligands: DTP.30 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:T.164 MG.31: 3 residues within 4Å: Chain P: T.164, L.251 Ligands: DTP.32 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:T.164

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

DTP.2: 16 residues within 4Å: Chain A: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.133, A:G.160, A:S.161, A:G.162, A:K.163, A:T.164, A:T.164, A:W.165, A:Y.310, A:S.331 Salt bridges: A:K.163, A:K.163, A:R.273 pi-Stacking: A:W.165, A:W.165, A:W.165 DTP.4: 16 residues within 4Å: Chain B: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.3 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.133, B:G.160, B:S.161, B:G.162, B:K.163, B:T.164, B:T.164, B:W.165, B:Y.310, B:S.331 Salt bridges: B:K.163, B:K.163, B:R.273 pi-Stacking: B:W.165, B:W.165, B:W.165 DTP.6: 16 residues within 4Å: Chain C: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.5 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:R.133, C:G.160, C:S.161, C:G.162, C:K.163, C:T.164, C:T.164, C:W.165, C:Y.310, C:S.331 Salt bridges: C:K.163, C:K.163, C:R.273 pi-Stacking: C:W.165, C:W.165, C:W.165 DTP.8: 16 residues within 4Å: Chain D: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.7 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:R.133, D:G.160, D:S.161, D:G.162, D:K.163, D:T.164, D:T.164, D:W.165, D:Y.310, D:S.331 Salt bridges: D:K.163, D:K.163, D:R.273 pi-Stacking: D:W.165, D:W.165, D:W.165 DTP.10: 16 residues within 4Å: Chain E: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.9 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:R.133, E:G.160, E:S.161, E:G.162, E:K.163, E:T.164, E:T.164, E:W.165, E:Y.310, E:S.331 Salt bridges: E:K.163, E:K.163, E:R.273 pi-Stacking: E:W.165, E:W.165, E:W.165 DTP.12: 16 residues within 4Å: Chain F: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.11 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:R.133, F:G.160, F:S.161, F:G.162, F:K.163, F:T.164, F:T.164, F:W.165, F:Y.310, F:S.331 Salt bridges: F:K.163, F:K.163, F:R.273 pi-Stacking: F:W.165, F:W.165, F:W.165 DTP.14: 16 residues within 4Å: Chain G: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.13 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:R.133, G:G.160, G:S.161, G:G.162, G:K.163, G:T.164, G:T.164, G:W.165, G:Y.310, G:S.331 Salt bridges: G:K.163, G:K.163, G:R.273 pi-Stacking: G:W.165, G:W.165, G:W.165 DTP.16: 16 residues within 4Å: Chain H: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.15 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:R.133, H:G.160, H:S.161, H:G.162, H:K.163, H:T.164, H:T.164, H:T.164, H:W.165, H:Y.310, H:S.331 Salt bridges: H:K.163, H:K.163, H:R.273 pi-Stacking: H:W.165, H:W.165, H:W.165 DTP.18: 16 residues within 4Å: Chain I: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.17 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:R.133, I:G.160, I:S.161, I:G.162, I:K.163, I:T.164, I:T.164, I:W.165, I:S.331 Salt bridges: I:K.163, I:K.163, I:R.273 pi-Stacking: I:W.165, I:W.165, I:W.165 DTP.20: 16 residues within 4Å: Chain J: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.19 15 PLIP interactions: 15 interactions with chain J Hydrogen bonds: J:R.133, J:G.160, J:S.161, J:G.162, J:K.163, J:T.164, J:T.164, J:W.165, J:S.331 Salt bridges: J:K.163, J:K.163, J:R.273 pi-Stacking: J:W.165, J:W.165, J:W.165 DTP.22: 16 residues within 4Å: Chain K: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.21 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:R.133, K:G.160, K:S.161, K:G.162, K:K.163, K:T.164, K:T.164, K:W.165, K:S.331 Salt bridges: K:K.163, K:K.163, K:R.273 pi-Stacking: K:W.165, K:W.165, K:W.165 DTP.24: 16 residues within 4Å: Chain L: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.23 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:R.133, L:G.160, L:S.161, L:G.162, L:K.163, L:T.164, L:T.164, L:W.165, L:S.331 Salt bridges: L:K.163, L:K.163, L:R.273 pi-Stacking: L:W.165, L:W.165, L:W.165 DTP.26: 16 residues within 4Å: Chain M: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.25 15 PLIP interactions: 15 interactions with chain M Hydrogen bonds: M:R.133, M:G.160, M:S.161, M:G.162, M:K.163, M:T.164, M:T.164, M:W.165, M:S.331 Salt bridges: M:K.163, M:K.163, M:R.273 pi-Stacking: M:W.165, M:W.165, M:W.165 DTP.28: 16 residues within 4Å: Chain N: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.27 15 PLIP interactions: 15 interactions with chain N Hydrogen bonds: N:R.133, N:G.160, N:S.161, N:G.162, N:K.163, N:T.164, N:T.164, N:W.165, N:S.331 Salt bridges: N:K.163, N:K.163, N:R.273 pi-Stacking: N:W.165, N:W.165, N:W.165 DTP.30: 16 residues within 4Å: Chain O: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.29 15 PLIP interactions: 15 interactions with chain O Hydrogen bonds: O:R.133, O:G.160, O:S.161, O:G.162, O:K.163, O:T.164, O:T.164, O:W.165, O:S.331 Salt bridges: O:K.163, O:K.163, O:R.273 pi-Stacking: O:W.165, O:W.165, O:W.165 DTP.32: 16 residues within 4Å: Chain P: A.127, Y.129, N.130, R.133, V.158, L.159, G.160, S.161, G.162, K.163, T.164, W.165, R.273, Y.310, S.331 Ligands: MG.31 15 PLIP interactions: 15 interactions with chain P Hydrogen bonds: P:R.133, P:G.160, P:S.161, P:G.162, P:K.163, P:T.164, P:T.164, P:W.165, P:S.331 Salt bridges: P:K.163, P:K.163, P:R.273 pi-Stacking: P:W.165, P:W.165, P:W.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, S. et al., Structure of the Drosophila apoptosome at 6.9 angstrom resolution. Structure (2011)

Release Date

2014-07-09

Peptides

Apaf-1 related killer DARK: ABCDEFGHIJKLMNOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Apaf-1 related killer DARK