SMTL ID : 6w6h.1

The Mycobacterium tuberculosis ClpB disaggregase hexamer structure in conformation II in the presence of DnaK chaperone and a model substrate

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

AGS.1: 15 residues within 4Å: Chain A: R.571, V.572, I.573, T.609, G.610, V.611, G.612, K.613, T.614, E.615, E.680, I.764, R.805, R.808 Chain B: R.746 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.573, A:T.609, A:G.610, A:V.611, A:V.611, A:G.612, A:K.613, A:T.614, A:T.614, A:E.615, A:E.615, A:R.808, B:R.746 Salt bridges: A:K.613, A:R.805, A:R.805 AGS.2: 15 residues within 4Å: Chain A: P.179, V.180, I.181, R.183, P.208, G.209, G.211, K.212, T.213, A.214, I.350, L.354 Chain B: A.329, R.332, R.333 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:I.181, A:G.209, A:G.211, A:K.212, A:K.212, A:T.213, A:A.214, B:R.333 Salt bridges: A:K.212, B:R.332, B:R.332 AGS.3: 17 residues within 4Å: Chain B: R.571, V.572, I.573, T.609, G.610, V.611, G.612, K.613, T.614, E.615, E.680, N.721, I.764, Q.768, R.805, R.808 Chain C: R.746 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:I.573, B:I.573, B:T.609, B:G.610, B:V.611, B:G.612, B:K.613, B:K.613, B:T.614, B:T.614, B:E.615, B:E.615, B:Q.768, B:R.808, C:R.746 Salt bridges: B:K.613, B:R.805, B:R.805 AGS.4: 16 residues within 4Å: Chain B: P.179, V.180, I.181, P.208, G.209, G.211, K.212, T.213, A.214, T.316, I.350, L.354, P.388 Chain C: A.329, R.332, R.333 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:I.181, B:I.181, B:G.209, B:G.211, B:K.212, B:K.212, B:T.213, B:A.214, B:T.316, C:R.333 Salt bridges: B:K.212, C:R.332, C:R.332 AGS.5: 16 residues within 4Å: Chain C: R.571, V.572, I.573, T.609, G.610, V.611, G.612, K.613, T.614, E.615, E.680, I.764, A.804, R.805, R.808 Chain D: R.746 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:I.573, C:I.573, C:G.610, C:V.611, C:G.612, C:K.613, C:K.613, C:T.614, C:T.614, C:E.615, C:E.615, C:R.808, D:R.746 Salt bridges: C:K.613, C:R.805, C:R.805 AGS.6: 17 residues within 4Å: Chain C: P.179, V.180, I.181, P.208, G.209, G.211, K.212, T.213, A.214, T.316, I.350, L.354, P.388, I.392 Chain D: A.329, R.332, R.333 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.178, 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, C:T.316 Salt bridges: C:K.212, D:R.332, D:R.332 AGS.7: 15 residues within 4Å: Chain D: R.571, V.572, I.573, T.609, G.610, V.611, G.612, K.613, T.614, E.615, I.764, Q.768, A.804, R.805, R.808 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:I.573, D:G.610, D:V.611, D:V.611, D:G.612, D:K.613, D:T.614, D:T.614, D:E.615, D:Q.768, D:R.805, D:R.808, D:R.808 Salt bridges: D:K.613 AGS.8: 15 residues within 4Å: Chain D: D.178, P.179, V.180, I.181, P.208, G.209, G.211, K.212, T.213, A.214, I.350, L.354, P.388, I.392 Chain E: R.332 10 PLIP interactions: 10 interactions with chain D 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 Salt bridges: D:K.212 AGS.11: 15 residues within 4Å: Chain A: A.329, R.332, R.333 Chain F: P.179, V.180, P.208, G.209, G.211, K.212, T.213, A.214, I.350, L.354, P.388, I.392 11 PLIP interactions: 7 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:V.180, F:G.209, F:K.212, F:T.213, F:T.213, F:A.214, A:R.332, A:R.332, A:R.333 Salt bridges: F:K.212, A:R.332 AGS.12: 17 residues within 4Å: Chain A: E.742, R.746 Chain F: R.571, V.572, I.573, T.609, G.610, V.611, G.612, K.613, T.614, E.615, E.680, Q.768, A.804, R.805, R.808 18 PLIP interactions: 17 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:I.573, F:T.609, F:G.610, F:V.611, F:V.611, F:G.612, F:G.612, F:K.613, F:K.613, F:T.614, F:E.615, F:E.615, F:E.680, F:Q.768, A:R.746 Salt bridges: F:K.613, F:R.805, F:R.805

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

ADP.9: 13 residues within 4Å: Chain E: D.178, P.179, V.180, I.181, P.208, G.209, V.210, G.211, K.212, T.213, A.214, I.350, P.388 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:D.178, E:V.180, E:E.207, E:G.209, E:V.210, E:G.211, E:K.212, E:T.213, E:T.213, E:T.213, E:A.214 Salt bridges: E:K.212 ADP.10: 13 residues within 4Å: Chain E: R.571, V.572, I.573, T.609, G.610, V.611, G.612, K.613, T.614, E.615, I.764, A.804, R.805 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:I.573, E:G.610, E:V.611, E:V.611, E:T.614, E:T.614, E:E.615, E:E.615 Salt bridges: E:R.805, E:R.805

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, Y. et al., Structural basis for aggregate dissolution and refolding by the Mycobacterium tuberculosis ClpB-DnaK bi-chaperone system. Cell Rep (2021)

Release Date

2021-05-26

Peptides

Chaperone protein ClpB: ABCDEF
Substrate: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
N

Chaperone protein ClpB

Substrate

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