SMTL ID : 5juy.1

Active human apoptosome with procaspase-9

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-7-7-4-mer

Ligands

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

DTP.1: 11 residues within 4Å: Chain A: V.125, F.126, V.127, C.158, G.159, K.160, S.161, V.162, R.265, P.321, Y.359 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.127, A:V.127, A:K.160, A:S.161, A:S.161, A:S.161, A:S.161, A:V.162, A:Y.359 Salt bridges: A:K.160, A:K.160, A:R.265 DTP.2: 11 residues within 4Å: Chain B: V.125, F.126, V.127, C.158, G.159, K.160, S.161, V.162, R.265, P.321, Y.359 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:V.127, B:V.127, B:K.160, B:S.161, B:S.161, B:S.161, B:S.161, B:V.162, B:Y.359 Salt bridges: B:K.160, B:K.160, B:R.265 DTP.3: 11 residues within 4Å: Chain C: V.125, F.126, V.127, C.158, G.159, K.160, S.161, V.162, R.265, P.321, Y.359 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:V.127, C:V.127, C:K.160, C:S.161, C:S.161, C:S.161, C:S.161, C:V.162, C:Y.359 Salt bridges: C:K.160, C:K.160, C:R.265 DTP.4: 11 residues within 4Å: Chain D: V.125, F.126, V.127, C.158, G.159, K.160, S.161, V.162, R.265, P.321, Y.359 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:V.127, D:V.127, D:K.160, D:S.161, D:S.161, D:S.161, D:S.161, D:V.162, D:Y.359 Salt bridges: D:K.160, D:K.160, D:R.265 DTP.5: 11 residues within 4Å: Chain E: V.125, F.126, V.127, C.158, G.159, K.160, S.161, V.162, R.265, P.321, Y.359 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:V.127, E:V.127, E:K.160, E:S.161, E:S.161, E:S.161, E:S.161, E:V.162, E:Y.359 Salt bridges: E:K.160, E:K.160, E:R.265 DTP.6: 11 residues within 4Å: Chain F: V.125, F.126, V.127, C.158, G.159, K.160, S.161, V.162, R.265, P.321, Y.359 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:V.127, F:V.127, F:K.160, F:S.161, F:S.161, F:S.161, F:S.161, F:V.162, F:Y.359 Salt bridges: F:K.160, F:K.160, F:R.265 DTP.7: 11 residues within 4Å: Chain G: V.125, F.126, V.127, C.158, G.159, K.160, S.161, V.162, R.265, P.321, Y.359 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:V.127, G:V.127, G:K.160, G:S.161, G:S.161, G:S.161, G:S.161, G:V.162, G:Y.359 Salt bridges: G:K.160, G:K.160, G:R.265

7 x HEC: HEME C(Non-covalent)

HEC.8: 25 residues within 4Å: Chain H: K.13, C.14, C.17, H.18, T.28, G.29, P.30, L.32, L.35, R.38, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.68, T.78, K.79, M.80, I.81, F.82, I.85, L.94 18 PLIP interactions: 18 interactions with chain H, Hydrophobic interactions: H:K.13, H:L.32, H:L.32, H:L.35, H:F.46, H:W.59, H:L.68, H:M.80, H:F.82, H:I.85 Hydrogen bonds: H:R.38, H:G.41, H:Y.48, H:Y.48, H:T.49, H:N.52, H:K.79 Metal complexes: H:H.18 HEC.9: 25 residues within 4Å: Chain I: K.13, C.14, C.17, H.18, T.28, G.29, P.30, L.32, L.35, R.38, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.68, T.78, K.79, M.80, I.81, F.82, I.85, L.94 18 PLIP interactions: 18 interactions with chain I, Hydrophobic interactions: I:K.13, I:L.32, I:L.32, I:L.35, I:F.46, I:W.59, I:L.68, I:M.80, I:F.82, I:I.85 Hydrogen bonds: I:R.38, I:G.41, I:Y.48, I:Y.48, I:T.49, I:N.52, I:K.79 Metal complexes: I:H.18 HEC.10: 25 residues within 4Å: Chain J: K.13, C.14, C.17, H.18, T.28, G.29, P.30, L.32, L.35, R.38, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.68, T.78, K.79, M.80, I.81, F.82, I.85, L.94 18 PLIP interactions: 18 interactions with chain J, Hydrophobic interactions: J:K.13, J:L.32, J:L.32, J:L.35, J:F.46, J:W.59, J:L.68, J:M.80, J:F.82, J:I.85 Hydrogen bonds: J:R.38, J:G.41, J:Y.48, J:Y.48, J:T.49, J:N.52, J:K.79 Metal complexes: J:H.18 HEC.11: 25 residues within 4Å: Chain K: K.13, C.14, C.17, H.18, T.28, G.29, P.30, L.32, L.35, R.38, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.68, T.78, K.79, M.80, I.81, F.82, I.85, L.94 18 PLIP interactions: 18 interactions with chain K, Hydrophobic interactions: K:K.13, K:L.32, K:L.32, K:L.35, K:F.46, K:W.59, K:L.68, K:M.80, K:F.82, K:I.85 Hydrogen bonds: K:R.38, K:G.41, K:Y.48, K:Y.48, K:T.49, K:N.52, K:K.79 Metal complexes: K:H.18 HEC.12: 25 residues within 4Å: Chain L: K.13, C.14, C.17, H.18, T.28, G.29, P.30, L.32, L.35, R.38, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.68, T.78, K.79, M.80, I.81, F.82, I.85, L.94 18 PLIP interactions: 18 interactions with chain L, Hydrophobic interactions: L:K.13, L:L.32, L:L.32, L:L.35, L:F.46, L:W.59, L:L.68, L:M.80, L:F.82, L:I.85 Hydrogen bonds: L:R.38, L:G.41, L:Y.48, L:Y.48, L:T.49, L:N.52, L:K.79 Metal complexes: L:H.18 HEC.13: 25 residues within 4Å: Chain M: K.13, C.14, C.17, H.18, T.28, G.29, P.30, L.32, L.35, R.38, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.68, T.78, K.79, M.80, I.81, F.82, I.85, L.94 18 PLIP interactions: 18 interactions with chain M, Hydrophobic interactions: M:K.13, M:L.32, M:L.32, M:L.35, M:F.46, M:W.59, M:L.68, M:M.80, M:F.82, M:I.85 Hydrogen bonds: M:R.38, M:G.41, M:Y.48, M:Y.48, M:T.49, M:N.52, M:K.79 Metal complexes: M:H.18 HEC.14: 25 residues within 4Å: Chain N: K.13, C.14, C.17, H.18, T.28, G.29, P.30, L.32, L.35, R.38, T.40, G.41, F.46, Y.48, T.49, N.52, W.59, L.68, T.78, K.79, M.80, I.81, F.82, I.85, L.94 18 PLIP interactions: 18 interactions with chain N, Hydrophobic interactions: N:K.13, N:L.32, N:L.32, N:L.35, N:F.46, N:W.59, N:L.68, N:M.80, N:F.82, N:I.85 Hydrogen bonds: N:R.38, N:G.41, N:Y.48, N:Y.48, N:T.49, N:N.52, N:K.79 Metal complexes: N:H.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, T.C. et al., A near atomic structure of the active human apoptosome. Elife (2016)

Release Date

2016-10-19

Peptides

Apoptotic protease-activating factor 1: ABCDEFG
Cytochrome c: HIJKLMN
Caspase-9: OPQR

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

Q
Q

R
R

Apoptotic protease-activating factor 1

Cytochrome c

Caspase-9

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