SMTL ID : 6rn3.1

ClpB (DWB mutant) bound to casein in presence of ATPgammaS - state WT-2A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

AGS.1: 15 residues within 4Å: Chain A: D.178, V.180, I.181, P.208, G.209, V.210, G.211, K.212, T.213, A.214, I.349, L.353, P.387, I.391 Chain F: R.331 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:D.178, A:I.181, A:I.181, A:G.209, A:K.212, A:K.212, A:T.213, A:T.213, A:T.213, A:A.214, A:T.315 Salt bridges: A:K.212, F:R.331, F:R.331 AGS.3: 19 residues within 4Å: Chain A: A.328, R.331, R.332 Chain B: D.178, P.179, V.180, I.181, P.208, G.209, G.211, K.212, T.213, A.214, T.315, I.349, L.353, P.387, D.388, I.391 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.178, B:I.181, B:I.181, B:G.209, B:G.211, B:K.212, B:K.212, B:T.213, B:T.213, B:T.213, B:A.214, B:T.315 Salt bridges: B:K.212, A:R.331, A:R.331 AGS.4: 18 residues within 4Å: Chain A: R.756 Chain B: R.569, V.570, I.571, G.572, T.607, G.608, V.609, G.610, K.611, T.612, E.613, D.677, N.719, Q.778, A.814, R.815, K.818 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:I.571, B:G.608, B:V.609, B:G.610, B:K.611, B:K.611, B:T.612, B:T.612, B:T.612, B:E.613, B:D.677, B:Q.778, B:K.818, A:R.756 Salt bridges: B:R.815, B:R.815, A:R.756 AGS.5: 17 residues within 4Å: Chain B: R.331, R.332 Chain C: D.178, P.179, V.180, I.181, R.183, P.208, G.209, G.211, K.212, T.213, A.214, I.349, L.353, P.387, I.391 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:D.178, C:I.181, C:I.181, C:G.209, C:G.211, C:K.212, C:K.212, C:T.213, C:T.213, C:T.213, C:A.214, C:Y.357 Salt bridges: C:K.212, B:R.331, B:R.331 AGS.6: 18 residues within 4Å: Chain B: R.756 Chain C: R.569, V.570, I.571, G.572, T.607, G.608, V.609, G.610, K.611, T.612, E.613, N.719, I.774, Q.778, A.814, R.815, K.818 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:I.571, C:G.608, C:V.609, C:G.610, C:K.611, C:K.611, C:T.612, C:T.612, C:T.612, C:E.613, C:N.719, C:Q.778, B:R.756 Salt bridges: C:K.611, C:R.815, C:R.815 AGS.7: 18 residues within 4Å: Chain C: R.331, R.332 Chain D: D.178, P.179, V.180, I.181, R.183, P.208, G.209, V.210, G.211, K.212, T.213, A.214, I.349, L.353, P.387, I.391 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.178, D:I.181, D:I.181, D:G.209, D:G.211, D:K.212, D:T.213, D:T.213, D:A.214 Salt bridges: D:K.212, C:R.331, C:R.332 AGS.8: 16 residues within 4Å: Chain C: R.756 Chain D: R.569, V.570, I.571, T.607, G.608, V.609, G.610, K.611, T.612, E.613, I.774, Q.778, A.814, R.815, K.818 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:I.571, D:I.571, D:G.608, D:V.609, D:G.610, D:K.611, D:K.611, D:T.612, D:E.613, D:Q.778, D:R.815, C:R.756, C:R.756 Salt bridges: D:K.611, D:R.815, D:R.815 AGS.9: 16 residues within 4Å: Chain D: R.331, R.332 Chain E: P.179, V.180, I.181, R.183, G.209, V.210, G.211, K.212, T.213, A.214, I.349, L.353, P.387, I.391 13 PLIP interactions: 1 interactions with chain D, 12 interactions with chain E Salt bridges: D:R.331, E:K.212 Hydrogen bonds: E:I.181, E:I.181, E:G.209, E:V.210, E:G.211, E:K.212, E:K.212, E:T.213, E:T.213, E:T.213, E:A.214 AGS.10: 19 residues within 4Å: Chain D: D.695, R.756 Chain E: R.569, V.570, I.571, G.572, T.607, G.608, V.609, G.610, K.611, T.612, E.613, L.766, I.774, Q.778, A.814, R.815, K.818 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:I.571, E:G.608, E:G.610, E:K.611, E:T.612, E:T.612, E:E.613, E:Q.778, E:K.818 Salt bridges: E:R.815

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.2: 14 residues within 4Å: Chain A: R.569, V.570, I.571, T.607, G.608, V.609, G.610, K.611, T.612, E.613, I.774, A.814, R.815, K.818 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:I.571, A:I.571, A:G.608, A:G.610, A:T.612 Salt bridges: A:K.611, A:R.815, A:R.815, A:K.818 ADP.11: 12 residues within 4Å: Chain F: V.180, I.181, P.208, G.209, V.210, G.211, K.212, T.213, A.214, I.349, L.353, I.391 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:I.181, F:I.181, F:V.210, F:G.211, F:K.212, F:T.213, F:T.213, F:T.213 Salt bridges: F:K.212, F:K.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deville, C. et al., Two-Step Activation Mechanism of the ClpB Disaggregase for Sequential Substrate Threading by the Main ATPase Motor. Cell Rep (2019)

Release Date

2019-07-03

Peptides

Chaperone protein ClpB: ABCDEF
casein: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
S

Chaperone protein ClpB

casein

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