SMTL ID : 6qs8.1

ClpB (DWB and K476C mutant) bound to casein in presence of ATPgammaS - state KC-2B

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

AGS.1: 18 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, I.349, L.353, P.387, I.391 Chain F: R.331 Ligands: MG.2 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:D.178, A:D.178, A:I.181, A:I.181, A:G.209, A:V.210, A:K.212, A:T.213, A:A.214 Salt bridges: A:K.212, F:R.331 AGS.3: 20 residues within 4Å: Chain A: R.331, R.332 Chain B: D.178, P.179, V.180, I.181, R.183, P.208, G.209, G.211, K.212, T.213, A.214, T.315, I.349, L.353, P.387, D.388, I.391 Ligands: MG.5 15 PLIP interactions: 10 interactions with chain B, 5 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:A.214, A:R.331, A:R.332, A:R.332 Salt bridges: B:K.212, A:R.331, A:R.331 AGS.4: 20 residues within 4Å: Chain A: R.756 Chain B: R.569, V.570, I.571, G.572, P.606, 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 Ligands: MG.6 15 PLIP interactions: 13 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:E.613, B:Q.778, B:R.815, A:E.752, A:R.756 Salt bridges: B:K.611, B:R.815, B:R.815 AGS.7: 18 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 Ligands: MG.9 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain C Hydrogen bonds: B:R.332, 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:A.214 Salt bridges: B:R.331, B:R.331, C:K.212 AGS.8: 18 residues within 4Å: Chain B: D.695, R.756 Chain C: 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 Ligands: MG.10 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:I.571, C:I.571, C:G.608, C:V.609, C:G.610, C:K.611, C:T.612, C:T.612, C:E.613, C:E.613, C:Q.778, B:R.756 Salt bridges: C:R.815, C:R.815 AGS.11: 19 residues within 4Å: Chain C: R.331, R.332 Chain D: D.178, 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, D.388, I.391 Ligands: MG.13 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.178, D:D.178, D:I.181, D:I.181, D:G.209, D:G.211, D:K.212, D:K.212, D:T.213, D:T.213, D:A.214 Salt bridges: D:K.212, C:R.331, C:R.331 AGS.12: 18 residues within 4Å: Chain C: 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, L.766, I.774, Q.778, R.815, K.818 Ligands: MG.14 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:I.571, D:G.608, D:V.609, D:V.609, D:G.610, D:K.611, D:T.612, D:E.613, D:E.613, D:Q.778, D:R.815, D:R.815, C:E.752, C:R.756 Salt bridges: D:K.611, D:R.815, D:R.815 AGS.15: 18 residues within 4Å: Chain D: R.331, R.332 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, I.349, L.353, P.387, I.391 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:D.178, E:D.178, E:I.181, E:I.181, E:G.209, E:G.211, E:K.212, E:K.212, E:T.213, E:T.213, E:T.213, E:A.214 Salt bridges: E:K.212, D:R.331, D:R.331 AGS.16: 21 residues within 4Å: Chain D: D.695, R.756 Chain E: R.569, V.570, I.571, G.572, P.606, T.607, G.608, V.609, G.610, K.611, T.612, E.613, I.774, I.777, Q.778, A.814, R.815, K.818 Ligands: MG.17 8 PLIP interactions: 1 interactions with chain D, 7 interactions with chain E Hydrogen bonds: D:R.756, E:I.571, E:G.608, E:G.610, E:T.612, E:E.613, E:R.815 Salt bridges: E:R.815 AGS.19: 15 residues within 4Å: Chain E: N.755, R.756 Chain F: I.571, T.607, G.608, V.609, G.610, T.612, E.613, R.631, I.774, Q.778, A.814, R.815, K.818 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:G.608, F:V.609, F:T.612, F:E.613, F:R.631, F:R.631, F:Q.778, E:N.755, E:R.756, E:R.756 Salt bridges: F:R.815, F:K.818

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.213 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.213 MG.5: 3 residues within 4Å: Chain A: R.332 Chain B: T.213 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.213 MG.6: 3 residues within 4Å: Chain B: T.612, D.677 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.612 MG.9: 2 residues within 4Å: Chain C: T.213 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.213 MG.10: 3 residues within 4Å: Chain C: T.612, D.677 Ligands: AGS.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.612 MG.13: 2 residues within 4Å: Chain D: T.213 Ligands: AGS.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.213 MG.14: 3 residues within 4Å: Chain D: T.612, D.677 Ligands: AGS.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.612, D:D.677 MG.17: 3 residues within 4Å: Chain E: T.612, D.677 Ligands: AGS.16 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.612

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

ADP.18: 17 residues within 4Å: Chain E: E.330, R.331 Chain F: P.179, V.180, I.181, E.207, P.208, G.209, V.210, G.211, K.212, T.213, A.214, I.349, L.353, P.387, D.388 13 PLIP interactions: 2 interactions with chain E, 11 interactions with chain F Hydrogen bonds: E:E.330, E:R.331, 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:D.388 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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