SMTL ID : 6oax.1

Structure of the hyperactive ClpB mutant K476C, bound to casein, pre-state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

9 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 21 residues within 4Å: Chain A: D.178, P.179, V.180, I.181, R.183, P.208, G.209, V.210, G.211, K.212, T.213, A.214, T.315, I.349, L.353, P.387, I.391 Chain E: T.198, A.328, R.331, R.332 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:D.178, A:D.178, A:I.181, A:I.181, A:G.209, A:G.211, A:K.212, A:K.212, A:T.213, A:T.213, A:T.213, A:A.214, A:Y.357, E:R.332 Salt bridges: A:K.212, E:R.331, E:R.331 AGS.2: 20 residues within 4Å: Chain A: R.569, V.570, I.571, P.606, T.607, G.608, V.609, G.610, K.611, T.612, E.613, E.678, N.719, L.766, I.774, Q.778, A.814, R.815, K.818 Chain E: R.756 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:I.571, A:G.608, A:V.609, A:V.609, A:G.610, A:K.611, A:K.611, A:T.612, A:E.613, A:E.613, A:E.613, A:E.678, A:N.719, A:R.815, E:R.756, E:R.756 Salt bridges: A:K.611, A:R.815, A:R.815 AGS.5: 21 residues within 4Å: Chain C: D.178, P.179, V.180, I.181, R.183, P.208, G.209, V.210, G.211, K.212, T.213, A.214, T.315, I.349, L.353, P.387, D.388, I.391 Chain D: A.328, R.331, R.332 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:D.178, C:I.181, C:I.181, C:G.209, C:V.210, C:G.211, C:K.212, C:K.212, C:T.213, C:T.213, C:A.214, D:A.328, D:R.331 Salt bridges: C:K.212, D:R.331, D:R.331 AGS.6: 21 residues within 4Å: Chain C: R.569, V.570, I.571, P.606, T.607, G.608, V.609, G.610, K.611, T.612, E.613, E.678, N.719, L.766, I.774, I.777, Q.778, A.814, R.815, K.818 Chain D: R.756 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.571, C:G.608, C:V.609, C:V.609, C:G.610, C:K.611, C:T.612, C:T.612, C:T.612, C:E.613, C:E.613, C:E.678, C:Q.778, C:R.815, C:R.815, D:R.756, D:R.756 Salt bridges: C:K.611, C:R.815, C:R.815 AGS.7: 21 residues within 4Å: Chain A: A.328, R.331, R.332 Chain D: P.179, V.180, I.181, R.183, P.208, G.209, V.210, G.211, K.212, T.213, A.214, E.279, T.315, I.349, L.353, Y.357, P.387, I.391 18 PLIP interactions: 6 interactions with chain A, 12 interactions with chain D Hydrogen bonds: A:A.328, A:R.331, A:R.332, A:R.332, D:I.181, D:R.183, D:G.209, D:V.210, D:G.211, D:K.212, D:K.212, D:T.213, D:T.213, D:A.214, D:Y.357 Salt bridges: A:R.331, A:R.331, D:K.212 AGS.8: 22 residues within 4Å: Chain A: E.752, R.756 Chain D: R.569, V.570, I.571, T.607, G.608, V.609, G.610, K.611, T.612, E.613, K.616, E.678, N.719, L.766, I.774, I.777, Q.778, A.814, R.815, K.818 23 PLIP interactions: 22 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:I.571, D:G.608, D:V.609, D:V.609, D:G.610, D:K.611, D:K.611, D:T.612, D:T.612, D:T.612, D:E.613, D:E.613, D:K.616, D:K.616, D:E.678, D:E.678, D:Q.778, D:R.815, A:R.756 Salt bridges: D:K.611, D:K.616, D:R.815, D:R.815 AGS.9: 22 residues within 4Å: Chain E: D.178, P.179, V.180, I.181, R.183, P.208, G.209, V.210, G.211, K.212, T.213, A.214, E.279, T.315, I.349, L.353, P.387, D.388, I.391 Chain F: A.328, R.331, R.332 15 PLIP interactions: 11 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:D.178, E:I.181, E:R.183, E:G.209, E:G.211, E:K.212, E:K.212, E:T.213, E:T.213, E:A.214, F:A.328, F:R.331 Salt bridges: E:K.212, F:R.331, F:R.331 AGS.10: 20 residues within 4Å: Chain E: R.569, V.570, I.571, P.606, T.607, G.608, V.609, G.610, K.611, T.612, E.613, E.678, N.719, L.766, I.774, Q.778, A.814, R.815, K.818 Chain F: R.756 21 PLIP interactions: 20 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:I.571, E:Q.573, E:T.607, E:G.608, E:V.609, E:V.609, E:G.610, E:K.611, E:K.611, E:T.612, E:T.612, E:T.612, E:E.613, E:E.613, E:E.678, E:E.678, E:Q.778, F:R.756 Salt bridges: E:K.611, E:R.815, E:R.815 AGS.11: 18 residues within 4Å: Chain B: R.331 Chain F: D.178, P.179, V.180, I.181, R.183, E.207, P.208, G.209, V.210, G.211, K.212, T.213, A.214, I.349, L.353, P.387, I.391 14 PLIP interactions: 11 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:D.178, F:I.181, F:I.181, F:G.209, F:V.210, F:G.211, F:K.212, F:T.213, F:T.213, F:A.214, B:R.331 Salt bridges: F:K.212, B:R.331, B:R.331

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

ADP.3: 9 residues within 4Å: Chain B: D.178, P.179, V.180, I.181, P.208, G.209, I.349, P.387, I.391 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.178, B:I.181, B:I.181, B:G.209 ADP.4: 13 residues within 4Å: Chain B: Q.573, G.608, V.609, T.612, E.613, R.631, H.764, I.774, Q.778, Y.812, A.814, R.815 Chain C: N.755 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.573, B:T.612, B:T.612, B:E.613, B:Q.778, C:N.755 Salt bridges: B:R.815, B:R.815 ADP.12: 14 residues within 4Å: Chain F: R.569, V.570, I.571, T.607, G.608, V.609, G.610, T.612, E.613, L.766, I.774, A.814, R.815, K.818 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:I.571, F:G.608, F:V.609, F:T.612, F:T.612, F:K.818, F:K.818 Salt bridges: F:R.815, F:R.815, F:K.818

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rizo, A.N. et al., Structural basis for substrate gripping and translocation by the ClpB AAA+ disaggregase. Nat Commun (2019)

Release Date

2019-06-12

Peptides

Hyperactive disaggregase ClpB: ABCDEF
Alpha-S1-casein: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
F

C
E

D
D

E
B

F
A

G
P

Hyperactive disaggregase ClpB

Alpha-S1-casein

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