SMTL ID : 5ofo.1

Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state, bound to the model substrate casein

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

AGS.1: 15 residues within 4Å: Chain A: P.183, V.184, E.211, P.212, G.213, V.214, G.215, K.216, T.217, A.218, I.353, L.357, P.391, I.395 Chain E: R.336 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:E.211, A:G.213, A:V.214, A:G.215, A:K.216, A:T.217, A:T.217, A:T.217, A:A.218, E:R.336, E:R.336 Salt bridges: A:K.216 AGS.2: 15 residues within 4Å: Chain A: R.573, V.574, I.575, G.612, V.613, G.614, K.615, T.616, E.617, I.778, A.818, R.819 Chain E: D.699, E.756, R.760 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:I.575, A:G.612, A:V.613, A:V.613, A:G.614, A:K.615, A:T.616, A:T.616, A:E.617, A:E.617, A:R.819, A:R.819, E:E.756, E:E.756, E:R.760 Salt bridges: A:R.819, A:R.819 AGS.3: 17 residues within 4Å: Chain B: P.183, V.184, I.185, R.187, E.211, P.212, G.213, V.214, G.215, K.216, T.217, A.218, I.353, P.391 Chain C: A.331, E.334, R.335 16 PLIP interactions: 4 interactions with chain C, 12 interactions with chain B Hydrogen bonds: C:E.334, C:E.334, C:R.335, B:I.185, B:R.187, B:R.187, B:G.213, B:V.214, B:G.215, B:K.216, B:T.217, B:T.217, B:T.217, B:A.218 Salt bridges: C:R.335, B:K.216 AGS.4: 12 residues within 4Å: Chain B: T.611, G.612, V.613, G.614, K.615, T.616, E.617, R.635, L.770, I.778, Q.782, R.819 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.612, B:V.613, B:K.615, B:T.616, B:T.616, B:E.617, B:R.635, B:Q.782, B:R.819 AGS.5: 15 residues within 4Å: Chain C: P.183, V.184, I.185, G.213, V.214, G.215, K.216, T.217, A.218, D.282, I.353, L.357, P.391, I.395 Chain D: R.335 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:I.185, C:I.185, C:G.215, C:K.216, C:T.217, C:T.217, C:A.218 Salt bridges: C:K.216, D:R.335 AGS.6: 14 residues within 4Å: Chain C: R.573, I.575, P.610, T.611, G.612, V.613, G.614, K.615, T.616, E.617, N.723, I.778, R.819 Chain D: E.756 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:I.575, C:I.575, C:G.612, C:V.613, C:G.614, C:K.615, C:T.616, C:T.616, C:T.616, C:E.617, C:E.617, C:E.617, D:E.756 Salt bridges: C:R.819, C:R.819 AGS.7: 19 residues within 4Å: Chain A: A.331, A.332, R.335, R.336 Chain D: P.183, V.184, R.187, E.211, P.212, G.213, V.214, G.215, K.216, T.217, A.218, I.353, L.357, P.391, D.392 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.187, D:E.211, D:G.213, D:V.214, D:G.215, D:K.216, D:T.217, D:T.217, D:T.217, D:A.218, A:A.331, A:R.336 Salt bridges: D:K.216 AGS.8: 14 residues within 4Å: Chain A: D.699, R.754, E.756 Chain D: R.573, I.575, T.611, G.612, V.613, G.614, K.615, T.616, E.617, T.721, I.778 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:G.612, D:G.614, D:K.615, D:T.616, D:T.616, D:T.616, D:E.617, D:E.617, A:E.756 Salt bridges: D:K.620, A:R.754 AGS.9: 14 residues within 4Å: Chain E: P.183, V.184, E.211, P.212, V.214, G.215, K.216, T.217, A.218, I.353, P.391, I.395 Chain F: R.335, R.336 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:E.211, E:G.215, E:K.216, E:T.217, E:A.218, F:R.336 Salt bridges: E:K.216 AGS.10: 15 residues within 4Å: Chain E: R.573, V.574, I.575, G.612, V.613, G.614, K.615, T.616, E.617, N.723, I.778, A.818, R.819 Chain F: D.699, R.760 15 PLIP interactions: 14 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:I.575, E:G.612, E:V.613, E:G.614, E:K.615, E:T.616, E:T.616, E:T.616, E:E.617, E:E.617, E:N.723, E:R.819, F:D.699 Salt bridges: E:K.615, E:R.819 AGS.11: 17 residues within 4Å: Chain B: R.335 Chain F: D.182, P.183, V.184, I.185, R.187, G.213, V.214, G.215, K.216, T.217, A.218, D.282, I.353, L.357, P.391, I.395 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:D.182, F:I.185, F:I.185, F:G.215, F:K.216, F:T.217, F:T.217, F:A.218, F:D.282 Salt bridges: F:K.216, B:R.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deville, C. et al., Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase. Sci Adv (2017)

Release Date

2017-08-16

Peptides

Chaperone protein ClpB,ATP-dependent Clp protease ATP-binding subunit ClpA,Chaperone protein ClpB: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
F

C
E

D
D

E
B

F
A

Chaperone protein ClpB,ATP-dependent Clp protease ATP-binding subunit ClpA,Chaperone protein ClpB

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