SMTL ID : 6djv.1

Mtb ClpB in complex with ATPgammaS and casein, Conformer 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

hetero-6-1-mer

Ligands

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

AGS.1: 16 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, N.721, A.804, R.805, R.808 Chain B: E.742, R.746 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.573, A:I.573, A:G.610, A:G.612, A:K.613, A:T.614, A:T.614, A:E.615, A:E.615, A:N.721, B:E.742, B:R.746 Salt bridges: A:R.805 AGS.2: 12 residues within 4Å: Chain A: P.179, V.180, I.181, G.211, K.212, T.213, A.214, E.279, T.316, L.354 Chain B: R.332, R.333 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.181, A:G.211, A:K.212, A:K.212, A:T.213, A:T.213, A:A.214, A:E.279 Salt bridges: A:K.212, B:R.332, B:R.332 AGS.3: 13 residues within 4Å: Chain B: R.571, V.572, I.573, G.610, V.611, G.612, K.613, T.614, E.615, N.721, R.805, R.808 Chain C: R.746 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:I.573, B:I.573, B:G.610, B:V.611, B:G.612, B:K.613, B:T.614, B:T.614, B:E.615, B:E.615, B:N.721 Salt bridges: B:R.805, B:R.805 AGS.4: 13 residues within 4Å: Chain B: P.179, V.180, I.181, P.208, G.209, G.211, K.212, T.213, A.214, L.354, D.389 Chain C: R.332, R.333 11 PLIP interactions: 9 interactions with chain B, 2 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, C:R.333 Salt bridges: B:K.212, C:R.332 AGS.5: 14 residues within 4Å: Chain C: R.571, V.572, I.573, G.610, V.611, G.612, K.613, T.614, E.615, N.721, A.804, R.805, R.808 Chain D: R.746 15 PLIP interactions: 1 interactions with chain D, 14 interactions with chain C Hydrogen bonds: D:R.746, C:I.573, C:I.573, C:G.610, C:V.611, C:G.612, C:K.613, C:T.614, C:T.614, C:T.614, C:E.615, C:E.615, C:N.721 Salt bridges: C:R.805, C:R.805 AGS.6: 15 residues within 4Å: Chain C: D.178, P.179, V.180, I.181, P.208, G.209, G.211, K.212, T.213, E.279, P.388, D.389, I.392 Chain D: R.332, R.333 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D 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:E.279, C:E.279 Salt bridges: C:K.212, D:R.332, D:R.332 AGS.7: 15 residues within 4Å: Chain D: R.571, I.573, T.609, G.610, V.611, G.612, K.613, T.614, E.615, E.680, I.764, Q.768, A.804, R.805, R.808 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:I.573, D:G.610, D:V.611, D:K.613, D:T.614, D:T.614, D:T.614, D:E.615, D:E.680, D:E.680, D:Q.768, D:R.805, D:R.808 AGS.8: 13 residues within 4Å: Chain D: D.178, V.180, I.181, G.209, V.210, G.211, K.212, T.213, A.214, L.354, P.388, D.389 Chain F: R.332 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:D.178, D:D.178, D:I.181, D:I.181, D:G.209, D:V.210, D:G.211, D:K.212, D:K.212, D:T.213, D:T.213, D:T.213, D:A.214 Salt bridges: D:K.212 AGS.11: 15 residues within 4Å: Chain A: D.697, R.746 Chain G: R.571, I.573, G.610, V.611, G.612, K.613, T.614, E.615, N.721, Q.768, A.804, R.805, R.808 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:I.573, G:I.573, G:G.610, G:V.611, G:G.612, G:K.613, G:T.614, G:T.614, G:T.614, G:E.615, G:N.721, G:Q.768, G:R.808, G:R.808 Salt bridges: G:R.805 pi-Cation interactions: G:R.808 AGS.12: 14 residues within 4Å: Chain A: R.332, R.333 Chain G: D.178, R.183, P.208, G.209, G.211, K.212, T.213, A.214, E.279, I.350, L.354, P.388 13 PLIP interactions: 10 interactions with chain G, 3 interactions with chain A Hydrogen bonds: G:D.178, G:D.178, G:G.182, G:G.209, G:G.211, G:K.212, G:T.213, G:T.213, G:E.279, A:R.332 Salt bridges: G:K.212, A:R.332, A:R.332

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

ADP.9: 11 residues within 4Å: Chain F: D.178, P.179, I.181, P.208, G.209, V.210, G.211, K.212, T.213, A.214, L.354 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:D.178, F:I.181, F:G.209, F:V.210, F:G.211, F:K.212, F:T.213, F:T.213, F:A.214 Salt bridges: F:K.212, F:K.212 ADP.10: 11 residues within 4Å: Chain F: I.573, T.609, G.610, V.611, G.612, K.613, T.614, I.764, Q.768, A.804, R.805 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:I.573, F:G.610, F:V.611, F:G.612, F:K.613, F:T.614, F:Q.768 Salt bridges: F:K.613, F:R.805, F:R.805

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, H. et al., ATP hydrolysis-coupled peptide translocation mechanism ofMycobacterium tuberculosisClpB. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-09-26

Peptides

Chaperone protein ClpB: ABCDFG
casein polyAlanine model: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
E

G
F

E
N

Chaperone protein ClpB

casein polyAlanine model

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