SMTL ID : 6dju.1

Mtb ClpB in complex with ATPgammaS and casein, Conformer 1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.80 Å

Oligo State

hetero-6-1-mer

Ligands

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

AGS.1: 13 residues within 4Å: Chain A: P.179, V.180, I.181, G.209, V.210, G.211, K.212, T.213, E.279, T.316, L.354 Chain B: R.332, R.333 13 PLIP interactions: 11 interactions with chain A, 2 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:T.213, A:T.213, A:E.279, A:E.279 Salt bridges: A:K.212, B:R.332, B:R.332 AGS.2: 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, N.721, R.805, R.808 Chain B: R.746 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.573, A:I.573, A:G.610, A:V.611, A:G.612, A:K.613, A:T.614, A:T.614, A:E.615, A:E.680, A:N.721, A:Q.768, B:R.746 Salt bridges: A:R.805 AGS.3: 13 residues within 4Å: Chain B: P.179, V.180, I.181, P.208, G.209, G.211, K.212, T.213, A.214, E.279, L.354 Chain C: R.332, R.333 13 PLIP interactions: 11 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:T.213, B:A.214, B:E.279 Salt bridges: B:K.212, C:R.332, C:R.332 AGS.4: 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 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain C 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:T.614, B:E.615, B:E.615, B:E.680, B:E.680, B:N.721, B:R.805, C:R.746 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, N.721, Q.768, A.804, R.805, R.808 Chain D: R.746 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:I.573, C:I.573, C:G.610, C:G.612, C:K.613, C:T.614, C:T.614, C:T.614, C:E.615, C:E.615, C:N.721, C:Q.768, D:R.746 Salt bridges: C:R.805, C:R.805 AGS.6: 13 residues within 4Å: Chain C: P.179, V.180, I.181, G.209, V.210, G.211, K.212, T.213, A.214, T.316, I.392 Chain D: R.332, R.333 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.181, C:I.181, C:G.209, C:G.211, C:K.212, C:T.213, C:T.213 Salt bridges: C:K.212, D:R.332, D:R.332 AGS.7: 12 residues within 4Å: Chain D: D.178, P.179, V.180, I.181, G.209, V.210, G.211, K.212, T.213, T.316, L.354 Chain F: R.332 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain F 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:T.213, D:T.316 Salt bridges: D:K.212, F:R.332 AGS.8: 14 residues within 4Å: Chain D: R.571, V.572, I.573, G.574, G.610, V.611, G.612, K.613, T.614, E.615, E.680, Q.768, R.805, R.808 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:I.573, D:G.610, D:V.611, D:G.612, D:K.613, D:T.614, D:T.614, D:E.615, D:E.680, D:Q.768, D:R.805, D:R.808 Salt bridges: D:K.613, D:R.805, D:R.805 AGS.9: 12 residues within 4Å: Chain F: D.178, P.179, V.180, I.181, P.208, G.209, V.210, G.211, K.212, T.213, A.214, P.388 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:D.178, F:D.178, F:V.180, F:G.209, F:V.210, F:G.211, F:K.212, F:T.213, F:T.213, F:T.213, F:A.214 Salt bridges: F:K.212 AGS.11: 12 residues within 4Å: Chain A: R.746 Chain G: R.571, V.572, I.573, G.610, V.611, G.612, K.613, T.614, E.615, R.805, R.808 15 PLIP interactions: 1 interactions with chain A, 14 interactions with chain G Hydrogen bonds: A:R.746, G:I.573, G:I.573, G:G.610, G:G.612, G:K.613, G:T.614, G:T.614, G:T.614, G:E.615, G:E.615, G:E.615, G:R.808, G:R.808 Salt bridges: G:R.805

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

ADP.10: 12 residues within 4Å: Chain F: R.571, T.609, G.610, V.611, G.612, K.613, T.614, E.615, Q.768, A.804, R.805, R.808 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:P.608, F:G.610, F:V.611, F:V.611, F:G.612, F:K.613, F:T.614, F:E.615, F:Q.768, F:R.808 Salt bridges: F:K.613, F:R.805, F:R.805 ADP.12: 12 residues within 4Å: Chain G: D.178, P.179, V.180, I.181, E.207, P.208, G.209, V.210, G.211, K.212, T.213, A.214 13 PLIP interactions: 13 interactions with chain G Hydrogen bonds: G:D.178, G:I.181, G:I.181, G:E.207, G:G.209, G:V.210, G:G.211, G:K.212, G:T.213, G:T.213, G:T.213, G:A.214 Salt bridges: G:K.212

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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