SMTL ID : 7xbk.1

Structure and mechanism of a mitochondrial AAA+ disaggregase CLPB

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-9-1-mer

Ligands

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

ATP.1: 19 residues within 4Å: Chain A: D.442, R.531 Chain B: I.317, I.318, S.352, S.353, G.354, I.355, G.356, K.357, T.358, E.359, Q.425, N.466, F.541, K.552, A.589, R.590 Ligands: MG.2 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.318, B:I.318, B:I.355, B:G.356, B:K.357, B:T.358, B:E.359, B:Q.425, B:Q.425, B:N.466, B:N.466 Salt bridges: B:K.357, B:K.357, B:R.590, B:R.590, B:R.590, A:R.531 ATP.4: 21 residues within 4Å: Chain B: H.343, D.442, E.527, R.531 Chain C: I.317, I.318, S.353, G.354, I.355, G.356, K.357, T.358, E.359, Q.425, N.466, F.541, L.549, A.589, R.590, K.593 Ligands: MG.3 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:I.318, C:I.318, C:G.354, C:I.355, C:G.356, C:K.357, C:T.358, C:E.359, C:Q.425, C:N.466, C:K.593 Salt bridges: C:K.357, C:K.357, C:R.590, C:R.590, C:R.590, B:R.531 ATP.6: 19 residues within 4Å: Chain C: D.442, R.531 Chain D: I.317, I.318, S.352, S.353, G.354, I.355, G.356, K.357, T.358, E.359, Q.425, N.466, F.541, L.549, A.589, R.590 Ligands: MG.5 19 PLIP interactions: 18 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:I.318, D:I.318, D:G.354, D:I.355, D:G.356, D:K.357, D:T.358, D:T.358, D:E.359, D:E.359, D:Q.425, D:N.466, D:N.466 Salt bridges: D:K.357, D:K.357, D:R.590, D:R.590, D:R.590, C:R.531 ATP.8: 18 residues within 4Å: Chain D: D.442, R.531 Chain E: H.316, I.317, I.318, G.354, I.355, G.356, K.357, T.358, E.359, Q.425, N.466, F.541, L.549, A.589, R.590 Ligands: MG.7 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:I.318, E:G.354, E:I.355, E:G.356, E:K.357, E:T.358, E:E.359, E:E.359, E:Q.425, E:N.466 Salt bridges: E:K.357, E:K.357, E:R.590, E:R.590, E:R.590, D:R.531 ATP.10: 22 residues within 4Å: Chain E: D.442, E.527, R.531 Chain F: I.317, I.318, S.352, S.353, G.354, I.355, G.356, K.357, T.358, E.359, Q.425, N.466, F.541, L.549, K.552, A.589, R.590, K.593 Ligands: MG.9 19 PLIP interactions: 18 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:I.318, F:I.318, F:G.354, F:I.355, F:G.356, F:K.357, F:T.358, F:T.358, F:T.358, F:E.359, F:E.359, F:Q.425, F:N.466, F:K.552 Salt bridges: F:K.357, F:R.590, F:R.590, F:R.590, E:R.531 ATP.12: 15 residues within 4Å: Chain F: D.442, R.531 Chain G: I.317, I.318, G.354, I.355, G.356, K.357, T.358, E.359, N.466, F.541, A.589, R.590 Ligands: MG.11 15 PLIP interactions: 1 interactions with chain F, 14 interactions with chain G Salt bridges: F:R.531, G:K.357, G:K.357, G:R.590, G:R.590, G:R.590 Hydrogen bonds: G:I.318, G:G.354, G:I.355, G:G.356, G:K.357, G:T.358, G:T.358, G:E.359, G:N.466 ATP.14: 19 residues within 4Å: Chain G: H.343, D.442, R.531 Chain H: I.317, I.318, S.352, S.353, G.354, I.355, G.356, K.357, T.358, E.359, L.360, F.541, L.549, A.589, R.590 Ligands: MG.13 13 PLIP interactions: 11 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:I.318, H:I.318, H:G.354, H:I.355, H:G.356, H:T.358, H:E.359, H:L.360, G:H.343 Salt bridges: H:K.357, H:K.357, H:R.590, G:R.531 ATP.15: 19 residues within 4Å: Chain H: H.343, D.442, R.531 Chain I: H.316, I.317, I.318, S.353, G.354, I.355, G.356, K.357, T.358, E.359, F.541, L.549, K.552, A.589, K.593 Ligands: MG.16 14 PLIP interactions: 12 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:I.318, I:G.354, I:G.356, I:K.357, I:T.358, I:T.358, I:E.359, I:E.359, I:K.552, I:K.593 Salt bridges: I:K.357, I:K.357, H:R.531, H:R.531

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.442 Chain B: T.358, Q.425 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.358 MG.3: 5 residues within 4Å: Chain B: R.531 Chain C: T.358, D.424, Q.425 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.358 MG.5: 3 residues within 4Å: Chain C: R.531 Chain D: T.358 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.358 MG.7: 5 residues within 4Å: Chain D: D.442 Chain E: T.358, D.424, Q.425 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.358 MG.9: 3 residues within 4Å: Chain E: R.531 Chain F: T.358 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.358 MG.11: 4 residues within 4Å: Chain G: G.356, K.357, E.359 Ligands: ATP.12 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain H: T.358, Q.425 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.358 MG.16: 4 residues within 4Å: Chain H: D.442, R.531 Chain I: T.358 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, D. et al., Comprehensive structural characterization of the human AAA+ disaggregase CLPB in the apo- and substrate-bound states reveals a unique mode of action driven by oligomerization. Plos Biol. (2023)

Release Date

2023-01-25

Peptides

Isoform 2 of Caseinolytic peptidase B protein homolog: ABCDEFGHI
Unknown peptide: J

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
L

Isoform 2 of Caseinolytic peptidase B protein homolog

Unknown peptide

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