SMTL ID : 3j9k.1

Structure of Dark apoptosome in complex with Dronc CARD domain

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-16-16-mer

Ligands

16 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 14 residues within 4Å: Chain A: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.125, A:V.125, A:R.127, A:G.154, A:S.155, A:G.156, A:K.157, A:T.158, A:W.159, A:S.325 Salt bridges: A:K.157, A:K.157 ADP.2: 14 residues within 4Å: Chain C: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:V.125, C:V.125, C:R.127, C:G.154, C:S.155, C:G.156, C:G.156, C:K.157, C:T.158, C:W.159, C:Y.304, C:S.325 Salt bridges: C:K.157, C:K.157 ADP.3: 14 residues within 4Å: Chain E: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:V.125, E:V.125, E:R.127, E:G.154, E:S.155, E:G.156, E:G.156, E:K.157, E:T.158, E:W.159, E:Y.304, E:S.325 Salt bridges: E:K.157, E:K.157 ADP.4: 14 residues within 4Å: Chain G: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:V.125, G:V.125, G:R.127, G:G.154, G:S.155, G:G.156, G:G.156, G:K.157, G:T.158, G:W.159, G:Y.304, G:S.325 Salt bridges: G:K.157, G:K.157 ADP.5: 14 residues within 4Å: Chain I: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 14 PLIP interactions: 14 interactions with chain I Hydrogen bonds: I:V.125, I:V.125, I:R.127, I:G.154, I:S.155, I:G.156, I:G.156, I:K.157, I:T.158, I:W.159, I:Y.304, I:S.325 Salt bridges: I:K.157, I:K.157 ADP.6: 14 residues within 4Å: Chain K: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:V.125, K:V.125, K:R.127, K:G.154, K:S.155, K:G.156, K:G.156, K:K.157, K:T.158, K:W.159, K:Y.304, K:S.325 Salt bridges: K:K.157, K:K.157 ADP.7: 14 residues within 4Å: Chain M: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 14 PLIP interactions: 14 interactions with chain M Hydrogen bonds: M:V.125, M:V.125, M:R.127, M:G.154, M:S.155, M:G.156, M:G.156, M:K.157, M:T.158, M:W.159, M:Y.304, M:S.325 Salt bridges: M:K.157, M:K.157 ADP.8: 14 residues within 4Å: Chain O: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 14 PLIP interactions: 14 interactions with chain O Hydrogen bonds: O:V.125, O:V.125, O:R.127, O:G.154, O:S.155, O:G.156, O:G.156, O:K.157, O:T.158, O:W.159, O:Y.304, O:S.325 Salt bridges: O:K.157, O:K.157 ADP.9: 14 residues within 4Å: Chain Q: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 14 PLIP interactions: 14 interactions with chain Q Hydrogen bonds: Q:V.125, Q:V.125, Q:R.127, Q:G.154, Q:S.155, Q:G.156, Q:G.156, Q:K.157, Q:T.158, Q:W.159, Q:Y.304, Q:S.325 Salt bridges: Q:K.157, Q:K.157 ADP.10: 14 residues within 4Å: Chain S: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 12 PLIP interactions: 12 interactions with chain S Hydrogen bonds: S:V.125, S:V.125, S:R.127, S:G.154, S:S.155, S:G.156, S:K.157, S:T.158, S:W.159, S:S.325 Salt bridges: S:K.157, S:K.157 ADP.11: 14 residues within 4Å: Chain U: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 12 PLIP interactions: 12 interactions with chain U Hydrogen bonds: U:V.125, U:V.125, U:R.127, U:G.154, U:S.155, U:G.156, U:K.157, U:T.158, U:W.159, U:S.325 Salt bridges: U:K.157, U:K.157 ADP.12: 14 residues within 4Å: Chain W: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 12 PLIP interactions: 12 interactions with chain W Hydrogen bonds: W:V.125, W:V.125, W:R.127, W:G.154, W:S.155, W:G.156, W:K.157, W:T.158, W:W.159, W:S.325 Salt bridges: W:K.157, W:K.157 ADP.13: 14 residues within 4Å: Chain Y: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 12 PLIP interactions: 12 interactions with chain Y Hydrogen bonds: Y:V.125, Y:V.125, Y:R.127, Y:G.154, Y:S.155, Y:G.156, Y:K.157, Y:T.158, Y:W.159, Y:S.325 Salt bridges: Y:K.157, Y:K.157 ADP.14: 14 residues within 4Å: Chain 0: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 12 PLIP interactions: 12 interactions with chain 0 Hydrogen bonds: 0:V.125, 0:V.125, 0:R.127, 0:G.154, 0:S.155, 0:G.156, 0:K.157, 0:T.158, 0:W.159, 0:S.325 Salt bridges: 0:K.157, 0:K.157 ADP.15: 14 residues within 4Å: Chain 2: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 12 PLIP interactions: 12 interactions with chain 2 Hydrogen bonds: 2:V.125, 2:V.125, 2:R.127, 2:G.154, 2:S.155, 2:G.156, 2:K.157, 2:T.158, 2:W.159, 2:S.325 Salt bridges: 2:K.157, 2:K.157 ADP.16: 14 residues within 4Å: Chain 4: Y.123, N.124, V.125, R.127, S.155, G.156, K.157, T.158, W.159, L.300, Y.304, P.321, R.322, S.325 12 PLIP interactions: 12 interactions with chain 4 Hydrogen bonds: 4:V.125, 4:V.125, 4:R.127, 4:G.154, 4:S.155, 4:G.156, 4:K.157, 4:T.158, 4:W.159, 4:S.325 Salt bridges: 4:K.157, 4:K.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pang, Y. et al., Structure of the apoptosome: mechanistic insights into activation of an initiator caspase from Drosophila. Genes Dev. (2015)

Release Date

2015-02-25

Peptides

Apaf-1 related killer DARK: ACEGIKMOQSUWY024
Caspase Nc: BDFHJLNPRTVXZ135

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

M
M

O
O

Q
Q

S
S

U
U

W
W

Y
Y

0
a

2
c

4
e

B
B

D
D

F
F

H
H

J
J

L
L

N
N

P
P

R
R

T
T

V
V

X
X

Z
Z

1
b

3
d

5
f

Apaf-1 related killer DARK

Caspase Nc